Massive unmelted Ti6Al4 V (Ti64) particles presented across all surfaces of additively manufactured Ti64 scaffolds significantly impacted the designed surface topography, mechanical properties, and permeability, reducing the osseointegration of the scaffolds. In this study, the proposed flowing acid etching (FAE) method presented high efficiency in eliminating Ti64 particles and enhancing the surface modification capacity across all surfaces of Ti64 scaffolds. The Ti64 particles across all surfaces of the scaffolds were completely removed effectively and evenly. The surface topography of the scaffolds closely resembled the design after the 75 s FAE treatment. The actual elastic modulus of the treated scaffolds (3.206 ± 0.040 GPa) was closer to the designed value (3.110 GPa), and a micrometer-scale structure was constructed on the inner and outer surfaces of the scaffolds after the 90 s FAE treatment. However, the yield strength of scaffolds was reduced to 89.743 ± 0.893 MPa from 118.251 ± 0.982 MPa after the 90 s FAE treatment. The FAE method also showed higher efficiency in decreasing the roughness and enhancing the hydrophilicity and surface energy of all of the surfaces. The FAE treatment improved the permeability of scaffolds efficiently, and the permeability of scaffolds increased to 11.93 ± 0.21 × 10 −10 mm 2 from 8.57 ± 0.021 × 10 −10 mm 2 after the 90 s FAE treatment. The treated Ti64 scaffolds after the 90 s FAE treatment exhibited optimized osseointegration effects in vitro and in vivo. In conclusion, the FAE method was an efficient way to eliminate unmelted Ti64 particles and obtain ideal surface topography, mechanical properties, and permeability to promote osseointegration in additively manufactured Ti64 scaffolds.