He was the President of American Academy of Dental Science and contributed in developing what is known as Margolis Cephalostat which is used in orthodontic diagnosis.
He then returned to Boston and joined the faculty of Harvard Dental School in addition to establishing his private practice in the city also.
While his stay in Boston, Margolis started working with Ernest Hooton, a noted anthropologist, on the cephalometric investigations looking at anatomy and evolution of the face.
He developed a maxillofacial triangle for analysis of cephalometric radiograph, where he selected spheno-occipital synchondrosis as a midcranial landmark due to it being last suture to fuse in the skull.
He was one of the first to point out the relationship between the lower incisors and the mandibular plane angle, a concept which was later adopted by Dr Charles H. Tweed.