This invention teaches methods of combining ion implantation steps with in situ or ex situ heat treatments to avoid and/or minimize implant-induced amorphization (a potential problem for source/drain (S/D) regions in FETs in ultrathin silicon on insulator layers) and implant-induced plastic relaxation of strained S/D regions (a potential problem for strained channel FETs in which the channel strain is provided by embedded S/D regions lattice mismatched with an underlying substrate layer). In a first embodiment, ion implantation is combined with in situ heat treatment by performing the ion implantation at elevated temperature. In a second embodiment, ion implantation is combined with ex situ heat treatments in a “divided-dose-anneal-in-between” (DDAB) scheme that avoids the need for tooling capable of performing hot implants.