I haven't seen any English tutorials that involve mesh alteration, so I decided to make one myself.
When using Metasequoia, there are a few important limitations to remember:
1) You can't change bones - so any animation is limited by existing parts. I know 3dsmax could feasibly get around this, but I don't own a copy.
2) No adding/deleting polygons! This will mess up the model in the game. If you want to remove anything, the best way to do this is to highlight the offending bit and hit >scale> set dimensions to zero. This makes the selection implode to 1 pixel, which you can hide inside the model. A better method is to use VRS, which doesn't mind deletion, but I dislike VRS because its camera is nonintuitive and laggorific. You can, however, add new polygons in VRS, although it's pretty troublesome to do so because it involves using metasequioa as VRS can't handle UV maps directly. Metasequioa mesh editing is limited, but MUCH faster.
So let's start with the basic project: Wings. Simple enough and often requested - but it's currently unknown to me precisely how to merge models/create bones and animation files so that you can get well-animated wings. You can make amateurish enough wings that are slightly functional in the game if you just use metasequioa though. In this case, I'll make a demon harness that looks like a demon harness. (to replace my ugly black/demon cloak, actually, but eh)
Pick an armour model with floating shoulder pads that are separate from the body. For this example I used chainmail as a base, but there are lots of others. There isn't much of a difference. BACK UP YOUR FILES. Modelviewer will do this for you, but play safe. I run both NA and JP versions of FFXI, so I have a mirror backup. =P
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Play around in Metasequioa with the move tool until you're familiar with how to shape objects. Using the shift key to select multiple vertices is very useful. If you need to move in one plane only, click on the corresponding coloured arrowhead and drag. After some practice, you should be able to unwrap the shoulders easily. Additionally, I made slight alterations to chest height and shaped the neck area into a collar, so don't worry if your model looks slightly different.
This bit usually takes the most amount of time: Examine the model animations in modelviewer and determine the angle at which to insert your wings. Try to select one where little clipping occurs in common animations (running, autoattack, chocobo). (Note: Hume male is a good model for wings because it doesn't have many animations which involve raising the arms above chest level. )
After you're happy with the mesh shape, it's time to apply base colour. Amadaun suggests drawing a plan beforehand, but I don't for several reasons:
-I'm generally too lazy. One reason I selected the chainmail model is because I wanted to reuse the chainmail texture.
-I prefer to make up the clothes as I go along, since I love last minute changes. rather than limiting design.
-Due to changes, said planned drawing usually ends up being ridiculously useless.
But whatever works for you - I prefer to start with specific troublesome areas. I find it's best to adjust the UV channels to your liking while you are colouring, if you can't edit UV channels in Metasequioa, delete the LE version you downloaded and get version 2.3.4.
Some people find it easier to abuse the burn tool, but it's MUCH safer to work on a separate layer - just create a new layer in photoshop and set it to multiply. The only problem is you'll need to know a bit about colours and photoshop to do this. The burn tool has a bad habit of changing the original hue you started with. The next picture shows how to do basic patchup work using copypaste and layers.
To test your colours quickly, I highly recommend the photoshop dds plugin, so you can import directly to modelviewer. This has the added benefit of leaving the bmp untouched, so you can retain "colour guides" using metasequioa. (see the red marks that let me know where to apply colour) - just select "Paint" in metasequioa (turn off basic mode under "File" first!), select an appropriately garish colour, then paint directly onto your 3d model > save. Open the bmp file in photoshop and voila - you have a colour guide that you can tack onto yet another layer while colouring!

I always add design detail last - doing otherwise makes you reluctant to delete and rework areas you spent much time on. This has an added benefit: An easy way to cheat is to use a slightly transparent layer set on overlay mode to paint designs. Also, you can easily change the patterns again if you ever feel like it.
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Final step is obviously to check what the model looks like in-game. Modelviewer does not accurately reflect what in-game models look like as it often gets alpha channels completely wrong. And there you have it - Wings. Easy!
Edit: I tried remapping both sides of the wings to different textures, but although this works in Metasequioa, it does not display correctly in the game. This means you're limited to having the same pattern on both the front and the back of your monodimensional meshes.
When using Metasequoia, there are a few important limitations to remember:
1) You can't change bones - so any animation is limited by existing parts. I know 3dsmax could feasibly get around this, but I don't own a copy.
2) No adding/deleting polygons! This will mess up the model in the game. If you want to remove anything, the best way to do this is to highlight the offending bit and hit >scale> set dimensions to zero. This makes the selection implode to 1 pixel, which you can hide inside the model. A better method is to use VRS, which doesn't mind deletion, but I dislike VRS because its camera is nonintuitive and laggorific. You can, however, add new polygons in VRS, although it's pretty troublesome to do so because it involves using metasequioa as VRS can't handle UV maps directly. Metasequioa mesh editing is limited, but MUCH faster.
So let's start with the basic project: Wings. Simple enough and often requested - but it's currently unknown to me precisely how to merge models/create bones and animation files so that you can get well-animated wings. You can make amateurish enough wings that are slightly functional in the game if you just use metasequioa though. In this case, I'll make a demon harness that looks like a demon harness. (to replace my ugly black/demon cloak, actually, but eh)
Pick an armour model with floating shoulder pads that are separate from the body. For this example I used chainmail as a base, but there are lots of others. There isn't much of a difference. BACK UP YOUR FILES. Modelviewer will do this for you, but play safe. I run both NA and JP versions of FFXI, so I have a mirror backup. =P

Play around in Metasequioa with the move tool until you're familiar with how to shape objects. Using the shift key to select multiple vertices is very useful. If you need to move in one plane only, click on the corresponding coloured arrowhead and drag. After some practice, you should be able to unwrap the shoulders easily. Additionally, I made slight alterations to chest height and shaped the neck area into a collar, so don't worry if your model looks slightly different.
This bit usually takes the most amount of time: Examine the model animations in modelviewer and determine the angle at which to insert your wings. Try to select one where little clipping occurs in common animations (running, autoattack, chocobo). (Note: Hume male is a good model for wings because it doesn't have many animations which involve raising the arms above chest level. )
After you're happy with the mesh shape, it's time to apply base colour. Amadaun suggests drawing a plan beforehand, but I don't for several reasons:
-I'm generally too lazy. One reason I selected the chainmail model is because I wanted to reuse the chainmail texture.
-I prefer to make up the clothes as I go along, since I love last minute changes. rather than limiting design.
-Due to changes, said planned drawing usually ends up being ridiculously useless.
But whatever works for you - I prefer to start with specific troublesome areas. I find it's best to adjust the UV channels to your liking while you are colouring, if you can't edit UV channels in Metasequioa, delete the LE version you downloaded and get version 2.3.4.
Some people find it easier to abuse the burn tool, but it's MUCH safer to work on a separate layer - just create a new layer in photoshop and set it to multiply. The only problem is you'll need to know a bit about colours and photoshop to do this. The burn tool has a bad habit of changing the original hue you started with. The next picture shows how to do basic patchup work using copypaste and layers.
To test your colours quickly, I highly recommend the photoshop dds plugin, so you can import directly to modelviewer. This has the added benefit of leaving the bmp untouched, so you can retain "colour guides" using metasequioa. (see the red marks that let me know where to apply colour) - just select "Paint" in metasequioa (turn off basic mode under "File" first!), select an appropriately garish colour, then paint directly onto your 3d model > save. Open the bmp file in photoshop and voila - you have a colour guide that you can tack onto yet another layer while colouring!

I always add design detail last - doing otherwise makes you reluctant to delete and rework areas you spent much time on. This has an added benefit: An easy way to cheat is to use a slightly transparent layer set on overlay mode to paint designs. Also, you can easily change the patterns again if you ever feel like it.

Final step is obviously to check what the model looks like in-game. Modelviewer does not accurately reflect what in-game models look like as it often gets alpha channels completely wrong. And there you have it - Wings. Easy!
Edit: I tried remapping both sides of the wings to different textures, but although this works in Metasequioa, it does not display correctly in the game. This means you're limited to having the same pattern on both the front and the back of your monodimensional meshes.
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