>>I don't see an option to not restore them as well when I try it in SSMS.
>
>Exactly, the only way would be to change the name of all the destinations. But, I ran out of space. So, I am making room now and will see how it goes.

I asked this question to one of my DBA friends to be sure. The answer is No, you can not remove NDF file when restoring.


There are ways to remove an empty .ndf file :
http://www.sqlmonster.com/Uwe/Forum.aspx/sql-server/9519/Remove-secondary-ndf-file