A few things I've learnt this week:
1. Scanning is tricky. Your art will rarely look the same after your scanner turns it into bits.
Get yourself a good scanner and see conclusion #2.
2. Photo editing software can be an artist's best friend. After scanning an illustration, you'll always feel the need to fix it somehow. This could mean adjusting its brightness or opacity, or even some sort of major intervention.
Conclusion: If you haven't done so already, download some photo editing software (you're definitely going to need it!). Some good choices are Gimp or Photoshop.
3. Learn from the pros. No matter what kind of artistic problem or difficulty you may trip over along the road, there's a good chance that someone else might have gone through that already.
Conclusion: Get your digital surfboard and surf the net (or your local library, if you dare to swim in deeper waters) to find out how others have solved this kind of problem. (I found some very useful tips about Removing Texture from Watercolor Scans at kidlitartists.blogspot.com.)