The advancement of nanoscience and technology relies on the development and utility of innovative techniques. Precise manipulation of photonic microcavities is one of the fundamental challenges in nanophotonics. This challenge impedes the construction of optoelectronic and photonic microcircuits. As a proof-of-principle, we demonstrate here that an atomic force microscopy cantilever and confocal microscopy can be used together to mechanically micromanipulate polymer-based whispering gallery mode microcavities or microresonators into well-ordered geometries. The micromanipulation technique efficiently assembles or disassembles resonators and also produces well-ordered dimer, trimer, tetramer, and pentamer assemblies of resonators in linear and bent geometries. Interestingly, an intricate L-shaped coupled-resonator optical waveguide (CROW) comprising a pentamer assembly effectively transduces light through a 90° bend angle. The presented new research direction, which combines mechanical manipulation and nanophotonics, is also expected to open up a plethora of opportunities in nano and microstructure-based research areas including nanoelectronics and nanobiology. This journal is © The Royal Society of Chemistry.