Techniques are provided for incrementally aligning multiple scans of a three-dimensional subject. This can be accomplished by establishing an updated aligned set of scans as each new scan is sequentially processed and aligned with the existing scans. In such embodiments the pairwise and global alignment processes are effectively combined into a single collective alignment process. This collective alignment converges to an optimal alignment faster than the sequential pairwise alignment process that existing solutions use. The collective alignment enforces pairwise alignment between the individual scans in the aligned set of scans. This is because each scan comprising the aligned set can be aligned to the next incremental scan if any scan included in the aligned set can be aligned to the next incremental scan. The pairwise alignment between the scans comprising the aligned set is thus a known function.