Nondestructive inspection of thick composite materials is important for maintaining manufacturing quality and structural integrity. Microwave nondestructive inspection methods are well suited for inspecting such structures, and offer many advantages compared to other nondestructive inspecting approaches. Optimization of microwave measurement parameters offers great versatility in detecting various sub-surface and surface defects while providing a high level of detection robustness. For this study two different thick composite specimens were used, one with a disbond (due to an embedded mylar sheet) having also generated some level of surface height variation in the specimen and the other subjected to an impact damage. An open-ended rectangular waveguide sensor was used to detect and distinguish between the defects and the surface height they may have produced in the specimens. With this probe suspended above the specimen and at a fixed operating frequency, the standoff distance was optimized for detection of the sub-surface defect (the mylar sheet) while nulling out the effect of surface height variations and the impact damage (and vice-versa). Microwave images of sample areas were produced for these optimization exercises effectively showing the surface height variations or the presence of the mylar sheet, respectively. A similar approach was employed to detect the surface height depression caused as a result of the impact damage on the second specimen. The result show that the choice of standoff distance can be optimally used to look for a surface or sub-surface defect while eliminating any influence due to specimen surface height variations (and vice-versa).