Trimming sequences manually involves adding an annotation of type Trim, with the special condition that this annotation can only be applied to the ends of a sequence:
double-click the sequence to trim in the Navigation Area | select the region you want to trim | right-click the selection | Trim sequence left/right to determine the direction of the trimming
This will add a trimming annotation to the end of the sequence in the selected direction. No sequence is being deleted here. Rather, the regions covered by trim annotations are noted by downstream analyses (in the same section of the Workbench Toolbox as the Trim tool) as regions to be ignored.