What renderer are you using? How is your material setup? You can have your Texture-Node and then two Image-Nodes. The second node is set to "copy alpha to rgb". This can be used in a phong or similar shader to set the transparency.
This should help: http://softimage.wiki.softimage.com/xsidocs/tex_maps_CreatingaTransparencyMap.htm You need to enable the "use alpha" checkbox in the transparency/reflection settings of the phong shader. Otherwise just use a second "image-node" and set it to "copy alpha to rgb" and connect it directly with the…