Shallow BF2and B implants (42 keV, 2×1015cm−2) were conducted at either liquid nitrogen or room temperature into deeply preamorphized (100) Si. Cross‐sectional transmission electron microscopy revealed that subsequent rapid thermal annealing (RTA) of the room‐temperature implanted BF2sample in the temperature range 950–1150 °C for 10 s created three classes of secondary defects at three different depth levels. The depths corresponded closely to the projected range of the BF2implant, the deep amorphous/crystalline interface, and the region immediately below the interface. In contrast, RTA of preamorphized Si with or without the shallow B implant both resulted in a high perfection surface region with secondary defects only in the region below the deep amorphous/crystalline interface. A phenomenological model for nucleation of the separate layers of defects is presented.