I believe you mean the ones in Slideshow in 5 minutes, under My Themes.

It's possible to remove and rename these custom templates, but it's a bit tricky. You need to remove (or rename) certain folders in the AppData directory. I suggest you back up this folder before following the steps.
Here are the steps:

1) Close SmartSHOW 3D if it's running.
2) To find the AppData folder, open Start and write %appdata%  in the Search box, then click Enter.
It will take you to the following path: “C:\Users\your username\AppData\Roaming”.
Now go to C:\Users\your username\AppData\Roaming\AMS Software\FotoShowPRO\Templates\Shows
3) Your themes are located in the User folder.
4) Inside this User folder, you'll find the folders with your themes. You may rename these folders or even delete them.
5) After this, run SmartSHOW 3D and check the Slideshow in 5 minutes menu.

If you need a detailed guide with screenshots, contact our tech support: http://smartshow-software.com/support.php

I understand this way is not that convenient, but our developers are now working on a better way for managing the custom slideshow themes. Once it's tested, it will be added in future updates.