We present a correlative study of structural and optical properties of natural defects in planar semiconductor microcavities grown by molecular beam epitaxy, which are showing a localized polariton spectrum as reported in Zajac et al., Phys. Rev. B 85, 165309 (2012). The three-dimensional spatial structure of the defects was studied using combined focussed ion beam (FIB) and scanning electron microscopy (SEM). We find that the defects originate from a local increase of a GaAs layer thickness. Modulation heights of up to 140 nm for oval defects and 90 nm for round defects are found, while the lateral extension is about 2µm for oval and 4µm for round defects. The GaAs thickness increase is attributed to Ga droplets deposited during growth due to Ga cell spitting. Following the droplet deposition, the thickness modulation expands laterally while reducing its height, yielding oval to round mounds of the interfaces and the surface. With increasing growth temperature, the ellipticity of the mounds is decreasing and their size is increasing. This suggests that the expansion is related to the surface mobility of Ga, which with increasing temperature is increasing and reducing its anisotropy between the [110] and [110] crystallographic directions. Comprehensive data consisting of surface profiles of defects measured using differential interference contrast (DIC) microscopy, volume information obtained using FIB/SEM, and characterization of the resulting confined polariton spectrum are presented.