The two-dimensional (2D) to three-dimensional (3D) morphology change in the highly strained growth of InAs on GaAs(001) is examined via in-situ, ultra-high vacuum (UHV) scanning tunneling microscopy (STM) and contact-mode atomic force microscopy (C-AFM). The formation of 3D InAs islands (˜2–4nm high) at an InAs delivery, θ˜1.57ML is found to be preceded by the appearance of small quasi-3D clusters (˜0.6–1.2nm high). The 2D to 3D transition is found to occur over a range of θ from ˜1.45ML to 1.74ML, with a varying and gradual mass transfer from 2D to 3D features with increasing θ. The InAs 3D islands are also examined in this study using non-contact AFM (NC-AFM) in order to assess the usefulness of this technique for imaging 3D features. Unlike the constancy observed in the C-AFM images, the NC-AFM images exhibit a marked imaging condition dependence. The variability observed in the NC-AFM images is qualitatively compared to the outcome of the simplest, force-gradient model of NC-AFM in order to extract a guideline for NC-AFM imaging of 3D features.