A regular expression search and replace can remove whitespace from the end of each line. Click Search, Replace then fill in the "Find what' field with [[:blank:]]+$ and leave the other field blank. Make sure the "use regular expressions" box is checked.
How the regular expression works:
[[:blank:]] matches a tab or a space
+ matches one or more occurances of the previous item
$ constrains the searches to the end of the line