Large substrate surface temperature decreases are observed during molecular beam epitaxy growth onto small indium bonded substrates, due to coating of the molybdenum block. These large temperature transients, along with other difficulties associated with indium bonding (e.g., potential substrate surface damage, unwanted indium on the back of the substrate) make indium free substrate mounting desirable, however, indium free mounting systems have previously been restricted to whole standard-sized round wafers. In this study we compare the temperature characteristics of new indium free modular substrate mounting blocks, which can accommodate substrates of various sizes (up to 3 inch diameter) and shapes, with traditional indium mounting of small substrates. Although the new modular indium free holders have a large molybdenum surface area exposed to the molecular beams, we find that the substrate surface temperature transients during growth are reduced to nearly negligible levels versus similar growth on indium bonded substrates, due to the effective thermal isolation of the substrate from the molybdenum. The real effects of these temperature differences observed by in situ pyrometry were confirmed by ex situ deep level transient spectroscopy (DLTS) measurements of homoepitaxial GaAs films, which show a two-to-three order of magnitude trap density increase in films grown on indium bonded substrates versus films grown on substrates mounted without indium bonding. This DLTS result is consistent with a real growth temperature difference between the two mounting techniques as was measured in situ by pyrometry.