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I assume you're using a IMAP account. You can unsubscribe folders you don't care about, to hide them and reduce visual clutter. They still exist, they're just ignored by Thunderbird. Right click on the accounts name in the folder pane and choose "subscribe" in the context menu. Then uncheck whatever folders you don't want to see and press the OK button.
If that has no effect go to the advanced section of the accounts server settings and check "Show only subscribed folders". That's normally checked by default. Normally these changes take effect immediately. If they don't exit and restart Thunderbird.
If none of this helps try exiting Thunderbird and deleting the "panacea.dat" and "xulstore.json" files in your profile. panacea.dat is a cache of known folders while xulstore,json stores the toolbar, window layout and size/position settings. The latter will be replaced by a file with default settings when you restart Thunderbird so you may need to customize your toolbars again.
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