Strain-free GaAs/AlGaAs semiconductor quantum dots (QDs) grown by droplet etching and nanohole infilling (DENI) are highly promising candidates for the on-demand generation of indistinguishable and entangled photon sources. The spectroscopic fingerprint and quantum optical properties of QDs are significantly influenced by their morphology. The effects of nanohole geometry and infilled material on the exciton binding energies and fine structure splitting are well-understood. However, a comprehensive understanding of GaAs/AlGaAs QD morphology remains elusive. To address this, we employ high-resolution scanning transmission electron microscopy (STEM) and reverse engineering through selective chemical etching and atomic force microscopy (AFM). Cross-sectional STEM of uncapped QDs reveals an inverted conical nanohole with Al-rich sidewalls and defect-free interfaces. Subsequent selective chemical etching and AFM measurements further reveal asymmetries in element distribution. This study enhances the understanding of DENI QD morphology and provides a fundamental three-dimensional structural model for simulating and optimizing their optoelectronic properties.