Tenami, if you make a screenshot of an item:
1) Use BMP or PNG file. If you use JPG it compresses the file and messes up an image. It's useless now.
2) Move cursor over a box where item lies, click on free space in the box so that cursor won't cover an item (right-lower corner is the best) and drag an item. Make a screenshot while dragging- this way you'll get rid of a item number counter.
(There are also few other methods for that. If item is compoundable you can just add it to compound screen and it will appear below the pot without a counter. Expressing should do that to I think)

Those two things are necessary to make an accurate item icon (without painting some "probable" pixels over item counter, or dealing with jpg compression marks).