Select Trim Whitespace in the Extra menu to remove whitespace from the start and the end of each line. If you selected part of the file, only lines that area selected will be trimmed. If not, all lines in the file will be trimmed.
If you've made a rectangular selection, EditPad Pro will only delete whitespace inside the rectangular block. Whitespace in the leftmost selected column and adjacent columns to the right will be deleted. Whitespace in the rightmost selected column and adjacent columns to the left will also be deleted.
Extra|Trim Leading Whitespace
Extra|Trim Trailing Whitespace
Extra|Delete Blank Lines
Extra|Consolidate Blank Lines