My server was flooded with spam, I am trying to remove thousands of files from the spool folders

I have created a new spool folder, and copied the spam filled ones.  I am trying to weed through the spam spool folders, do I need to copy both the eml and the corresponding hdr file to the new good spool folder. Or can I just copy the .eml files?  I can do a search for the compromised email that sent all the spam, but It wont search .hdr files in windows.