There are two types of scenes on my HTC incredible from Verizon: Scenes that I've created and the built-in scenes (Verizon Scene, HTC, Social, Work, Play, Travel, and Clean Slate)
Deleting the user defined scenes is fairly straightforward, although it's non-intuitive. Go to: Menu->Settings->Personalize->scenes. Long press on the scene to be deleted and a pop-up menu comes up asking to Rename or Delete. That's pretty easy.
Deleting the built-in, pre-loaded scenes is more work, but I discovered yesterday how to do it, so I wanted to share that here. There may be other ways to achieve the same end, but I'll show how I did it. Note, that you must have root permissions to do this, and if you break something, it's not my fault.
All of the scenes are stored in a SQLite database in /data/data/com.htc.launcher.databases/. The database is launcher.db. I used Root Exploer to go to /data/data/com.htc.launcher and copy the databases folder first for backup purposes. Then I used SQLite Editor to edit the launcher.db database file. There are 6 tables in the database:
The table to edit is widget_workspaces. It'll have a list of all of the scenes, both user defined and built in. Long press on each scene to delete and a pop-up menu will be shown. Click Delete Record to remove the scene. The phone must be rebooted for the change to take effect. I removed all of the built-in scenes successfully with-out seeing any ill-effects from the change. Now, the only scenes on the phone are the ones I want and not the ones the verizon/htc want me to have.