The influence of strain and temperature on the development of 3D island growth patterns (wavy layer growth) and the establishment of a defined modulation period in epitaxially grown multiple quantum well structures of the III–V compound alloys is discussed. Experimental evidence for a previously derived theoretical roughening transition curve, which separates 2D monolayer from 3D island growth is presented. In this paper we furthermore derive the f 2 ∼ λ −1 relationship between misfit strain f and modulation wavelength λ, and give experimental evidence. Ultra-high resolution scanning transmission electron microscopy (STEM) analysis is performed in the above alloys to investigate the occurrence of alloy inhomogeneities. In parallel, highly dislocated regions in the multiple quantum well (MQW) stacks are systematically studied by transmission electron microscopy (TEM). The latter two investigations are undertaken in order to establish possible nucleation sites and to better understand the nucleation process for the 3D growth mode.