We established an in-plane microfabrication process of polymeric AFM micropipettes that include a microchannel with an aperture at the apex without further processing after wafer scale lithography. The channel was obtained by etching a sacrificial electrochemically plated copper layer. Such sideways fabrication scheme offers the possibility of designing various types of cantilevers with different shapes and lengths within a single wafer, such as a length of 500 µm or being connected by two triangular hollow tips. The probes were operated in optical beam deflection AFM mode. First, force-indentation curves were measured on substrates with different stiffness, and then microbeads were spatially manipulated in a hydrogel showing their reusability in case of clogging. Finally, we succeeded in using such probes to carry out cell-isolation experiments of neurons cultured in vitro (2D layers) and in hydrogels (3D architecture).