Harvard is one of the world's largest repositories of manuscripts and archives. Most of Harvard's collections are represented in HOLLIS, but for an in depth search for manuscripts at Harvard, you should talk with the librarians at the likely Harvard repositories.
HOLLIS searches catalog records and online finding aids. Finding aids are searched full text and the associated catalog record is displayed with a link to the finding aid. Many archival collections have catalog records only, with their finding aids existing only in paper in their repository. Search in Library Catalog Advanced Search, adjusting Resource type tpo Archives/Manuscripts.
A limited number of finding aids which are very long are not fully indexed. Only the first ~80K words are indexed. (Affects ~ 115 finding aids, or 2%).
HOLLIS for Archival Discovery (the successor to OASIS) searches the full text of the finding aids (only, no catalog records)). It retrieves whole collections (listed at the top of the results), then components of collections, usually individual items (sometimes digital) or series.
Collect Subject terms from pertinent records as you do keyword searches and look for related Subject terms. Subject terms for organizations are often useful in finding personal papers. The record for the John Warren papers bears the terms "Warren, John, 1753-1815" and "Harvard Medical School Curricula". The term "medical" occurs in the Summary field. Subject searches on medicine, physicians, or surgeons will not retrieve the record for the John Warren papers.
Archival Collections - Harvard Graduate School of Design
Houghton Library: A Student's Guide
Schlesinger Library on the History of Women in America (open link for Schlesinger)