Lately, I've been deeply immersed in hair meshing, and I've built about 15 hairmeshes. But unfortunately, only few of them are usable because of the transparency issue. According to this tutorial (http://www.modthesims.info/showthread.php?p=3268345), transparency issues can be recognized by 'blue lines' in milkshape. I checked my mesh, and it's full of those blue lines...and I also checked NewSea's hair mesh out of sheer curiosity, and I found something that I never dreamed I would find..... Blue lines! NewSea's mesh were full of them(look at the screenshot). I'm pretty shocked about this, because NewSea's hairs have no transparency issues at all when viewed in game....Does anybody know why NewSea's hairs have no transparency issues when it should have them?

While those lines may indicate areas that may have issues in-game, the way Milkshape renders is very different from in-game. Just because there are transparency issues in Milkshape doesn't mean there will be any in-game.

Actually Newsea's hairs do have a lot of transparency issues, see the dark gray lines on the edges of the stands in the picture? Those are transparency issues that would relate to the blue lines in your picture (even though they're different hairs, I'm using Morning Dew as an example). It's not the typical "giant holes of doom" type of transparency issues but it definitely still is a transparency issue. You have to look more closely at her hairs in game. Point is that you should minimize the blue in your hairs as much as possible. Realistically though small issues like this aren't very noticeable in game and aren't a humongous deal.

edit: forgot pic

To make sure you are viewing the transparency issues properly, right click the Viewport and uncheck "Draw Backfaces".

While making the mesh we need make the backfaces ourselves, that option is to force the Milkshape engine to render the backfaces itself.
And in case of a already built mesh, with the backfaces already made it's not necessary, as it will make the engine render backfaces of both base mesh as well, the backfaces.

To understand why those horrible things happen to meshes you need to understand the rendering process.
Each geometry is build with vertices, each of those vertices have an ID, a number that identifies them along their position for the render.
While rendering, the game engine will draw those vertices and align as they are saved, and in case a vertex is "above" other that is located before of it, the engine while applying the Alpha Reference will draw it in front of the lower one. That is what causes that issue.

For example, backfaces always must be before the base geometry itself, because of this.
You need to look at your geometry and identify which one goes before of the other.
That means, in the Milkshape group list, those that are below every other geometry is at first on the list, while the other who are above all other geometries should be at the bottom.

The concept isn't hard, but you get the hang of it. Hope it helped!

Thanks for the answer :D. But I'm wondering....there seems to be a limit to simply moving group orders in milkshape, especially on complex hairs. So is there a way to prevent this? I use blender 3d to mesh my hairs.

A limit? can you be more specific?

For instance, There is a strand which comes out frome the top and it encircles another strand that is below it. In cases like these, simply moving the groups doesn't seem to do the trick

Yes, that's true, some complex meshes are difficult to work with. You'd either have to separate those strands so it is possible to arrange them, or live with the transparency issues.

This problem is actually the engine's fault, it's not smart enough to calculate each vertex.
I don't blame the developers since The Sims is a really big and complex game already.

In that case you need to be strategical, understand that you will not find a easier way to fix that, because some vertex can overlap others on different angles as well.
So, when you are making your hair meshes make sure you follow the logic. It's bad I know, since we can't make all the detail we want.
But it's an unfortunate problem, and at certain styles inevitable. And becomes a huge limitation of the freedom we have with our geometries unfortunately.

Happy meshing!

Oh.. okay. Thanks whiterider and MarkJS :D. That made everything clear.

Just a little more note on that, before we close this subject.
You don't need to always avoid this problem by doing the meshes another way.
There are other ways to work around that, but it requires more patience.
For example, as you mentioned, a little strand comes from the top and evolves through another plane.

In that specific case, if you really want to fix it, what you can do is to select the faces where it evolves behind other plane and click on "Regroup".
By doing that, all the selected faces will be into this new group, which you can move down to the geometry it goes behind.
It's a lot of work sometimes, I know, but if you want it to be free of problems you need to make attention of it.
Meshing is a test of patience, specially when it's about to fix those.

Forgive me, as I missed one step on what I've said last.

Before clicking "Regroup" on Milkshape, Go to the Menu Vertex > Unweld, this will unweld (separate) the selected vertices from the base mesh.
Then click "Regroup" to send the vertex selection to a new group.
As you are unwelding, it might have some mismatch on the game.
In Maya usually it looks fine, but that is due how the game renders and applies the UV along with the texture.

Try selecting only the part where the plane is not affected by a full-white Alpha Reference.

If you h8 the opacity issues you can also uvmap each layer seperate(usinge a bigger texture file)