Editing the alpha of the material file will give transparency but if u look closer, the effect is created by many small pixel of the color u chose ("dot matrix" effect). To make the effect less obvious, u can increase the polygon count of your mesh. There is another method that is using BGEM file instead of BGSM. Doing so u will not have the "dot matrix" effect but this is more for "glass type" transparency. If what u working on is not "glass type", the effect will not be nice/good if u using the BGEM method. 

As for making a certain part of texture invisible, add a "NiAlphaProperty" to your mesh (nif) and using transparency at your diffuse texture map. There is another method of doing this by using "Vertex Color".