Interconnection technologies utilizing metal-coated polymer microspheres (MPS) offer promising solutions for applications with fine-pitch, high-density interconnects. The capability of controlling position and number of MPS in individual interconnects is considered the key to further realize these technologies in emerging applications where large dies with an extremely high number of ultra fine-pitch input/output pins and/or temperature-sensitive substrates are often involved. This paper introduces an innovative approach for the deposition of MPS, ranging from 4.8 to 40 µm, onto patterned substrates for advanced interconnection technologies. We investigate how key process parameters, including assembly temperature, deposition speed, trap geometry, and trap spacing affect deposition yield and precision. Our results show that the highest deposition yield (~100%) is achieved at a substrate temperature of around 45 °C. Larger particles require higher assembly speeds, while trap size determines the number of particles captured. For consistent results, a trap spacing of 2.5 times the particle size is necessary. This study also demonstrates the feasibility of the proposed approach for interconnection technologies that require fine-pitch, low temperature, and low pressure conditions.