If you prefer Paint.NET, you can also use it instead of the GIMP (
little tutorial on deleting backgrounds in Paint.NET for cartoonimator91 - Flash format, about 120 kB).
Note: Paint.NET automatically exports an alpha channel to PNGs where the background is transparent.
The GIMP is more complete and has a lot more options and useful stuff, but can occasionally be confusing or intimidating to beginners.
It doesn't matter which program you use, the important part is that (1) it exports to PNG, and (2) the PNG has a transparent background (alpha channel).
Note:
Anime Studio is not, unfortunately, a mind reader - it cannot guess which parts of your drawn character are movable limbs drawn in front of the body, or what the arm hidden behind the body looks like, or what the leg partly hidden behind the other leg looks like.
To effectively use a scanned hand-drawn character or photo, you're going to break it into separate parts, either when you draw it or in an image-editing program like Paint.NET or the GIMP, before you import the parts into Anime Studio.
See the very end of the little tutorial linked above for a very simple example of a broken apart character.
Regards, Myles.