Blue line trouble... I had the same problem early on. I was a bit mercenary with the pencil issue. I found a process that sometimes eliminates the use of them entirely.
This sketch was done digitally on my iPad on sketchbook pro. I printed it out on 11x17 image and used a light box to render my final image in ink. If I had to sketch out anything, it was very light and easily erased.
In short, pencils and I don't get along. I'm too much of a neat freak.
There may be several solutions to your problem so here we go...
if you do want to continue using that blue pencil, I would suggest making much lighter strokes. Take the pencil and draw with the side of your hand, like your doing a sketch. A lighter tone of the blue should not show up on the scanner. Don't try to RENDER with the pencil. Just use it to show where you want your shapes to go. I also have found other artists that use a 4H pencil instead, and then go over with a darker pencil.
You may want to recalibrate the scanner or adjust the scanning to a lighter setting so it's not picking up all the noise of the blue pencil. Some scanning software allow for that.
Are you scanning in black and white or in grayscale? Grayscale picks up EVERYTHING. You want to use the b&w setting when there is blue line on the page. Or, you can adjust the brightness and contrast after its been scanned in, if you have photoshop.
Let me know if any of this helps. always feel free to ask anything. Happy to help.
Maybe I should get better scanning software, I dunno, but I've seen fully rendered pages done in blue line and inked and the final prints looked fine. I have no idea how to get mine to turn out that well. I wish I had something in my gallery as an example...
I would, but my gallery hasn't been updated in so long precisely for the reason that I'm not longer working with my own scanner, my own software... nothing really. It's kind of a stressed living situation until my wife and I can get a new apartment. Maybe soon.
Been there, dude. The first half of this year, I went to staples once a week for scanning and printing. Lol. It can be done, but it's a pain. Consider it a testament to your dedication to the craft! Lol