Hi,
from one source system how many entries(records) you have?
at master data level, have you used source system object as compounded? if yes then you can delete the data thru below program.
if you have more data from your source system(which want delete) then selective deletion(manually) will be time consuming one.
So check report/SE38 - RSDMDD_DELETE_BATCH.
Use proper selections and delete the data which is specific to your source.
Assumed as you delete transaction data related to your source.
Thanks