Two‐photon polymerization (2PP) is a versatile microfabrication tool for biomedical applications as it provides unparalleled resolution for accurate three‐dimensional (3D) replication of biological microstructures. To widen the selection of biomaterials suitable for 2PP, this paper presents the processing of a methacrylated poly(ε‐caprolactone)‐based oligomer (PCL‐o) and a poly(ethylene glycol) diacrylate (PEGda) hydrogel into microstructures. PCL‐o is a novel biodegradable photopolymer that has not been previously processed with 2PP, and the fabrication of both polymers with an Nd:YAG laser is reported here for the first time. The overall 2PP processability and achievable resolution were studied by polymerizing arbitrary microstructures on glass substrates. The samples were characterized with scanning electron microscopy. Additionally, the effect of photoinitiator concentration on the resolution was investigated. Also, a preliminary cell attachment test was performed with UV cured films in order to investigate the impact of the used material–initiator combination on cell viability and migration. As a result, laser‐induced polymerization of both PCL‐o and PEGda was successfully demonstrated, and the Nd:YAG laser was proven adequate for the 2PP processing of the novel biodegradable photoresist. Resolution in the order of 1 µm was achieved with PCL‐o. With the easy processing of both PEGda and PCL‐o, these materials have great potential for different biomedical applications. Copyright © 2011 John Wiley & Sons, Ltd.