You've import a mesh to Milkshape but it looks broken on 3D? But it looks fine on 2D view? That's mean that there's something wrong on the viewport.
How to fix it?
- First, go to C:\Users\USERNAME\AppData\Roaming\MilkShape 3D 1.x.x (If you're using Windows 7, I don't know if you're using other Windows version). - Then look some files called "viewport0.cfg" until "viewport3.cfg" (maybe you'll find more) and delete them all. - Restart Milkshape and (if you have a good luck) you'll find that the 3D function is back to normal.