Purpose: Recently, a novel approach to apicoectomy has emerged, involving the use of a hollow trephine with a surgical guide. This innovative technique creates a semicircular section, in contrast to the conventional straight cut (with a bur). The semicircular shape of this section raises questions about the method’s effectiveness in eliminating supernumerary canals (SNCs), which are auxiliary canals alongside the main root canal. These canals pose a risk of further infection if not thoroughly eliminated. The aim of this exploratory study was to assess the efficacy of the proposed method in the removal of SNCs. Methods: A sample of 200 extracted single-rooted human teeth was rigorously narrowed down by multiple steps to 33 specimens that contained SNCs in the apical third. These specimens underwent apical semicircular sectioning, removing the apical 3 mm of the root. The specimens then underwent repeated CT scanning. For samples with residual SNCs, the section was transformed into a straight section and another CT scan was performed. Results: The semicircular section eliminated all SNCs in 94% of the specimens, and it eliminated 97.3% of the SNCs in all specimens. The straight-line sectioning eliminated 98.6% of all SNCs and eliminated all SNCs in 96.97% of the SNC-containing teeth. Conclusions: The efficacy of semicircular apicoectomy performed with a trephine appears to be comparable (χ2 = 1.00, df = 1, and p = 0.317) to that of the conventional straight apicoectomy performed with a bur as reported in the literature.