Thanks Ramah for your offer to send the layer. That would help a lot.

Using more layers for the mountains: Actually I tried that last night and worked pretty well. Another idea I had was making the brushes with white background. That way the white would cover the mountains in the back. Then I would select all the white color in the layer (with Select -> Color Range -> Highlighted, or some other way) and delete it. But I haven't used that yet and don't know if it works.

I'd like to know if you know any other way I could use for selecting the mountains from the image.
Last night I tried Select -> Color Range -> Sampled colors (or something like that) after selecting a color close to the mountain color. This path allowed me to select even the thinner lines, but the clearing process took 15 min for one brush because of the detail it had.