Texture pack Minecraft transparent blocks?

When I create a texturepack for Minecraft and edit weapons with a higher resolution, the page blocks become transparent. I work with paint.net

LG and thanks for the answers

Usually not, but I've never tried it either

Take the wand tool and click with it next to the textures of the weapons. Then press DELETE *. If you can still see transparent pixels, increase the tolerance and do it * again.