Apparatus for fluorescence-based single photon generation includes collection optics and various setups for characterization. This can have complexity when tweaking in one part changes the optimal alignment of everything. We suggest here a modular system, where each compartment is given the optimal alignment and has independent self-tests. Based on this concept, we built a stable and extendable system for single photon generations with fluorescence center in nano-flakes. The system has advantages of extending the number of single mode fiber output, which are connected to various external setups for analysis and reserved for practical uses as a photon source in radiometry. Another benefit is a high level of stability to preserve the optimal condition with the help of internal self-tests in each module. For demonstrations, we had a crystal-defect fluorescence center in hexagonal boron nitride nano-flake, and produced a single photon stream qualified by the single photon factor g (2) (0) = 0.25 and the maximum count rate of 3 × 10 5 per second at a saturation point. Due to high stability, we prolonged a single photon stream over an hour with uniform count rates.