1) First create a new folder and name it processed.
2) Open with irfanview and open batch conversion.
3) Open add all the textures to be converted and set the destination output folder. Set to BMP and go to advanced.
4) Change color depth with these options (the source images here already have dithering so I am leaving that option unchecked)
5) Start the batch.
6) Drag and drop all the processed images into a new Half-life format WAD. Open the image you want to have transparency.
7) Select background with eyedropper and observe the palette selection.
5) Go to colors>edit palette and with the color you selected with the eyedropper set the color to RGB 0 0 255.
6) Now go to colors>translate colors and set the source index to the destination of 255 with "swap indexes checked"
7) Close and save the image and now rename it by putting { infront of the filename. Save the wad and import into hammer/jackhammer
8) Now Texture your brush and change it to func_wall or func_illusionary and set the render mode to texture with FX amount to 255.