Owing to the superior dielectric property of aluminum oxide, precise patterning of self-assembled monolayers (SAMs) and nanoparticles (NPs) on aluminum oxide substrates is highly interesting for generating SAM- or NP-based electronic devices. This study employed nanoimprint lithography (NIL) and nanomolding in capillaries (NAMIC) for patterning ferromagnetic NPs on aluminum oxide substrates. We demonstrated the fabrication of structured arrays of various SAMs and NPs in micrometre and nanometre ranges. The polymer template generated by NIL behaved as a physical barrier and defined the pattern areas on the substrate. FePtAu NPs were assembled on phosph(on)ate SAM-modified polymer patterned substrates. After polymer removal, nano- and microscale line and dot NP patterns, with controlled layer thickness, were obtained on aluminum oxide substrates. Thick nanolines of NPs were obtained by NAMIC. PO3-terminated FePtAu NPs were assembled on alumina without need of a linker. The magnetic properties of the NPs were addressed by vibrating sample magnetometry and those of the patterned NPs by magnetic force microscopy.