U.S. National Library of Medicine has a search page that aggregates online resources. The History of Medicine Finding Aids Consortium is a discovery tool that provides keyword search services across a union catalog of descriptions of primary sources materials found in special collections and archives throughout the United States.
The consortium leads to information found in historical documents, personal papers, business records, and other sources. Finding aids provide contextual information about these collections along with detailed inventories to help researchers locate relevant materials. Currently 3,600 finding aides are indexed from 35 institutions that collect broadly in the areas of the history of medicine, allied sciences, general collections and archives.
Here is the link to the initial search page: National Library of Medicine. A keyword search, 'American Civil Medicine', yielded 233 record collections and their web links.