The typical dimensions of bacterial and microorganism cells match well with the scales at which nanomaterial-based architectures can influence the environment. However, it is one of the most formidable challenges to achieve designed patterns at the microscale for studying microorganisms. Here, we present a method to recognize and locate motile microorganisms at the microscale. The micro-printing strategy via droplet manipulation achieves functional molecule patterning with accurate positions and orientations at the microscale. It is controlled under the interplay between the macroscopic driving forces and the microscopic interfacial dynamics. Photoluminescence patterns have the character of shape matching and uniform light guiding for phototactic microorganisms. The strong attraction among motile microorganisms and photoluminescence patterns prompts microscale artificial selection and location, which will promote the development of self-organized bio-patterning.