How to Draw Simple Tilesets - So You Don't Have An Excuse Anymore

When I make grass, I did exactly what you did, but then the original color I draw over is still there and when I make use of the tileset it ends up like this.
How do I fix it? I tried to make it white and I tried to make it black but still with no success. I also tried to take away the color using Rectangle select and then Move Selected Pixels, but it didn't work. (I use Paint.NET)

You have a problem as I see.
Who can fix it? Me!
To fix the transparency of its,
Make the bit depth 32 bits.
Then make your grass and trees!

Thank you! Gives a

Another program I'd recommend for tileset creation is Aseprite. The current version (at time of posting) is $10, but you can grab version 0.9.5 for free and it works just as well as the paid version (give or take a few features).