What type of object and what dont you want the shader to effect?
Making the alpha channel in GIMP:
1. Use levels instead. Easier to deal with at first.
2. First make sure you add an alpha channel to your image. Right click on the layer and choose add alpha channel in the channels dialog it will show all white or alpha 255.
3. Select the places you want to change the alpha on.
4. Choose colors levels. the levels dialog opens.
5. Change the channel to alpha.
6. In the output levels slider part. Move the white side towards 0. You will see the transparency grid starts to show.
7. Stop where you want the alpha to be. Example: 128. Press ok.
8. Notice in the channels dialog that the alpha channel now contains a grey area of the selection you made.
Save you texture as .dds with compression levels at dxt3 compression.
You now have an alpha channel in your image.
Intel(R) Core(TM)2 Quad CPU Q6600 @ 2.40GHz, 2400 Mhz, 4 Core(s), 4 Logical Processor(s), 8gb RAM, Nvidia gtx660, Windows 7 Pro 64bit, Screen resolution 1680 x 1050.