Select Trim Trailing Whitespace in the Extra menu to remove whitespace from 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 rightmost selected column and adjacent columns to the left will be deleted. This whitespace needn't be at the end of the line. If a line is short and doesn't extend to the rightmost selected column, any whitespace at the end of the line covered by the selection will be deleted.
Extra|Trim Leading Whitespace
Extra|Delete Blank Lines
Extra|Consolidate Blank Lines