( CUT FOR LARGE PICTURES )SO HERE'S OUR WORKSPACE! You can see all the cropped images up in the corner there (this is one aspect of paint.NET that drives me nuts because you have to scroll through them all the time) and a nice base of Dr. Theo to make into an icon. The first thing I'm going to do is get rid of all of that background stuff.
You can see I've started erasing it here (or rather, painting over it with white), the only part to be careful about is around the lines you're keeping so you don't mess any of them up. Adjust your brush size as necessary to get into tight spots. With the zoom, you can also see better the grainyness of the image since it's not the best quality scan. But since this is black and white we can fix that easily!
Once you've cleaned up, open up your Brightness/Contrast panel (under Adjustments or Ctrl+Shift+C) and change the settings to your liking. I usually go with Brightness between -10 and 10 depending on the lighting, and Contrast 20-25 to clean up the grey noise.
Usually then I'll tighten up your crop a bit more. I stick to increments of 10 or 20 to make sure it resizes smoothly, and don't go any smaller than 150-160, because past that it'll start to get a bit blurry when you resize. Here I went with 200. Once you have your selection, use Crop To Selection (Ctrl+Shift+X) and Resize to 100x100 (Ctrl+R)
This part is optional but it's easy and imo makes the icons look a lot more polished so I recommend doing it. Make a new layer and create a greyscale radial gradient on it. (If you haven't done gradients in paint.NET before, click where you want the center of the gradient to be and drag it out til the colors are to your liking.) Note that I'm using a grey instead of black, that way I don't have to fiddle with opacity in the next step.

After you've done that, open up your layer properties (that's the little icon with the pencil in the bottom right of your layers panel) and change the Blending Mode to Multiply. This looks a bit nicer than just the stark black and white, and should also remove any remaining noise there might be on the white. Then just hit ok and save it!
SIDE NOTE; both to save time and to keep the icons looking consistent, I suggest pasting the gradient layer as a new image, and just keeping it on your clipboard and pasting it as a new layer (Ctrl+Shift+V) onto each image instead of creating a new layer.
THAT'S IT! I hope this was helpful to some people!? You can use this methods for other things too, really. All I add for my Dangan Ronpa spirte icons is a flat color background, and boost the Saturation (Adjustments-> Hue/Saturation or Ctrl+Shift+U; I usually set it to 110-120) and use the same sort of gradient overlay.