Here's a fail-proof method:

1: Save a copy of your tileset and erase all areas you want to be unmasked.
2: Turn the brightness/contrast all the way up or down, so that your tileset's solid remains are 1 color (black or white).
3: Replace the black or white with a single bright color (like pink or blue).
4: Make a new palette and fill all colors except 0 and 1 with this single bright color.

Oh and last but not least, try to avoid pure black, it'll be transparent. Use (for example) the darkest possible shade of blue to prevent this.