I know this has been covered in other posts, but I've yet to find one that answers this for me. I use illustrator to convert hand-drawn line images (sketched on paper) which have been scanned into AI files.  I use Image trace to create the vector graphic and then the usual steps to reveal the lines using the pen tool and making the mask transparent.  Thats easy. What I want to be able to do is draw the lines, then have the hand color in the fill.  How do you accomplish this so it look clean?  

You use the same process on the fills that you use on the line art (transparent stroked paths)

If you want different results, attach the SVG file and explain more clearly what you want to fix.

-Mike (videoscribe user)