High threading dislocation densities limit the operability of infrared focal plane arrays based on large lattice-mismatched heterostructures such as HgCdTe/CdTe/Si. Recently it has been shown that post-growth thermal cycle annealing can routinely reduce the surface etch pit density from >5 x 10(6) cm(-2) to as low as 9 x 10(5) cm(-2). To fully exploit the procedure, a deeper understanding of the inherent dislocation dynamics is needed. In this work, we employ scanning transmission electron microscopy to analyze cross-sectional samples of HgCdTe/CdTe/Si prepared using site-specific focused ion beam milling. A key factor in this work is the use of defect decorated samples, which has allowed for a correlation of surface etch pits to dislocation segments observed in cross-section images. We have observed that the previously reported oval-shaped etch pits are likely associated with Shockley partial type dislocations, and that triangular etch pits are associated with perfect dislocations. This suggests the likelihood that interaction between mobile Shockley partial and other dislocation types are responsible in part for the observed reduction in top surface etch pit density. These studies provide a deeper understanding of dislocation reduction processes which are critical for the realization of high performance infrared detectors based on low-cost, lattice-mismatched substrates. Published by Elsevier B.V.