PBase

My Nikon Coolscan 9000 seems to do a poor job of scanning 35mm negatives and slides. The scans have lots of noise. I can make it better using Noise Ninja, but they're still not wonderful. The scanner does much better with 6x6 negatives.

Has anyone had a similar experience? Am I doing something wrong?

To get rid of noise try this:

Are there updates for the Nikon Scan software?
Make sure the Firewire cable stays away from any Power cable
Clean off any dust on the film with a hand blower
Film is emulsion side down in carrier

Auto Exposure for Negative Film when scanning Negatives
No Auto Exposure when scanning Slides
Multi-Sampling 16x
Digital Ice - Normal
Auto Focus
Save as TIFF

Everything else is is turned off or not used - do your sharpening/etc with photoshop

Hope this helps your scans look better.