Abrupt, stable, and high-density doping of semiconductors is critical in semiconductor fabrication, particularly in scaling transistors to single-nanometer size. Microwave annealing emerges as a promising solution, offering efficient and stable dopant activation in heavily doped semiconductor wafers with an abrupt dopant profile. Compared to conventional thermal annealing, microwave annealing can directly interact with the dopant with minimal lattice heating to prevent broadening of the dopant profile and formation of unstable dopant-defect clusters. For instance, in epitaxial silicon doped above the solubility of phosphorus, a common challenge arises from compensating most phosphorus dopants with vacancies. Some of these phosphorus-vacancy clusters can become mobile around 700 °C, further diminishing doping efficiency. The proposed prototype microwave annealer addresses these challenges by enabling uniform, direct annealing without the need for a susceptor. Comprising a waveguide with its dielectric properties matched to that of the sample to be annealed, the prototype annealer is optimized based on 3D full-wave finite-element electromagnetic simulation. The prototype annealer selectively activates metastable phosphorus-vacancy clusters by interacting with their dipole moments while preventing lattice heating above 700 °C. This approach facilitates efficient and stable doping in heavily doped semiconductors, thus contributes to the advancement in semiconductor device scaling.