The transparent conducting oxide (TCO) ZnO:Al is often used as the window layer and a source of light trapping in thin-film silicon solar cells. Light scattering in sputtered zinc oxide is achieved by wet chemical etching, which results in craters distributed randomly over the ZnO surface. To gain a better understanding of the etching process on ZnO thin films, a method for atomic force microscope (AFM) realignment between etching steps is developed. Using this method, the evolution of the HCl etch on a polycrystalline ZnO thin-film is observed. Results showed that this observation method did not modify the etching behavior, nor did stopping and restarting the etching change the points of attack, indicating that the points of HCl attack are built into the films as they are grown. Additionally, we investigated the evolution of the HCl etch on a ZnO surface previously etched in KOH, and found that the etch sites for both the acidic and basic solution are identical. We conclude that “peculiar” defects, which induce accelerated etching, are built into the film during growth, and that these defects can extend part or all the way though the thin-film in a similar way as screw dislocations in single crystalline ZnO.