Highly c-axis orientated sputter deposited aluminium nitride (AlN) thin films are widely used as piezoelectric layers in micro-electro-mechanical systems (MEMS). Therefore, stable and reliable deposition and patterning of the AlN thin films in the fabrication process of such devices is of utmost importance. In this work, we study the wet chemical etching behavior of highly c-axis oriented AlN layers as well as the film-related residuals after the etching procedure. To investigate the impact of the underlying material on the quality of the AlN films they are either deposited on pure silicon (Si) substrates or on Si substrates covered with a sputter-deposited thin titanium (Ti) film. The 620 nm thin AlN layers are synthesized simultaneously onto both substrate types and subsequently wet-chemical etched in a phosphorous acid based etching solution at a temperature of 80°C. We demonstrate a significant difference in surface roughness of the untreated AlN films when sputter-deposited on Ti or pure Si. Furthermore, we analyze the piezoelectric properties of the deposited films. Although the XRD analyses indicate a high c-axis orientated wurtzite structure for all deposited films, the absolute value of the piezoelectric coefficients |d33| of AlN thin films synthesized on Ti are 0.4-4.3 pC/N, whereas corresponding values of 5.2-6 pC/N are determined at those deposited on pure Si substrates,. Finally, after wet chemically etching a porous, but homogeneous AlN microstructure is observed for samples synthesized onto Ti layers, whereas AlN layers deposited directly on Si substrate are either etched very inhomogenously or almost completely with some etch resistant pyramidal-shaped residues. This might be due to a local change in polarity within the AlN layer.