Yes, you can!
To trim your trace, head directly to the sequence or topology map of your DNA sequence. Highlight the number of bases you wish to delete and press the "delete" button on your keypad.
Once you have trimmed your trace(s), open up the alignment you wish to realign. Simply press the blue "Realign" in the top bar towards the lefthand side of your window. When the pop-up box appears, press the green "realign" button at the bottom of the box. The sequences will then realign according to the modified traces.