The aim of this study was to compare root trunk measurements taken parallel to the tooth axis (TA) to those taken parallel to the root surface (RS) in order to assess the decision-making implications of each method on crown-lengthening surgery. A total of 672 root trunks were measured via CBCT in two planes: TA and RS. The possibility of performing crown lengthening in each clinical situation based on the distance from the cementoenamel junction (CEJ) to the crestal bone (CB) after ostectomy (CEJ-CB) was judged and compared between groups. When RS was used as a reference point, the proportions of cases that judged crown lengthening to be possible were 83.63%, 59.08%, and 39.18% for CEJ-CB values of 4, 5, and 6 mm, respectively. When TA was used instead, those proportions decreased by 3.87% to 7.29%. The lingual root trunk of the lower first molar (LFL) with a CEJ-CB of 4 to 5 mm emerged as the most problematic area; here, the difference between reference planes occurred with one out of every six teeth. Within the limits of this study, utilizing TA for surgical crown-lengthening treatment planning is not ideal because it may lead to extraction of many savable teeth.