Addressing the challenge of efficient drug delivery to the lungs, a nano-structured, microparticulate carrier system with defined and customizable dimensions has been developed. Utilizing a template-assisted approach and capillary forces, particles were rapidly loaded and stabilized. The system employs a biocompatible alginate gel as a stabilizing matrix, facilitating the breakdown of the carrier in body fluids with the subsequent release of its nano-load, while also mitigating long-term accumulation in the lung. Different gel strengths and stabilizing steps were applied, allowing us to tune the release kinetics, as evaluated by a quantitative method based on a flow-imaging system. The micro-cylinders demonstrated superior aerodynamic properties in Next Generation Impactor (NGI) experiments, such as a smaller median aerodynamic diameter (MMAD), while yielding a higher fine particle fraction (FPF) than spherical particles similar in critical dimensions. They exhibited negligible toxicity to a differentiated macrophage cell line (dTHP-1) for up to 24 h of incubation. The kinetics of the cellular uptake by dTHP-1 cells was assessed via fluorescence microscopy, revealing an uptake-rate dependence on the aspect ratio (AR = l/d); cylinders with high AR were phagocytosed more slowly than shorter rods and comparable spherical particles. This indicates that this novel drug delivery system can modulate macrophage uptake and clearance by adjusting its geometric parameters while maintaining optimal aerodynamic properties and featuring a biodegradable stabilizing matrix.