Nasoalveolar molding (NAM) is commonly employed to reduce the alveolar segments into proper alignment and to improve nasal symmetry in patients with cleft lip and palate. This study examines the periodical progression of NAM treatment over time. 20 patients with complete unilateral cleft lip and palate were prospectively recruited. A 2 stage NAM treatment protocol was applied. Stage 1 involved adjustment of the alveolar segments (mean age 15.6 days), while Stage 2 added nasal stents and started average 43 days after stage 1. 3D images (n = 241) were obtained prior to NAM initiation and weekly until the end of treatment. The cleft lip area, bilateral nostril areas, and the nostril height and width were measured. Treatment was assessed in the Cleft (C) side and the Non-cleft (N). There was significant difference in the C/N ratio of the nostril area, width, and height at pre-treatment (0.9 ± 0.3, 4.1 ± 1.1, and 0.5 ± 0.2), at the end of stage 1 (1.1 ± 0.3, 2.2 ± 0.6, and 0.8 ± 0.2), and at the end of stage 2 treatment (1.8 ± 0.3, 1.8 ± 0.4, and 1.2 ± 0.1); p < 0.05. Comparative 3D analysis with dense sampling offers a precise methodology for showing effects of NAM treatment. The morphological changes achieved with NAM therapy occur in early treatment phase.