The B4 helical nanofilament (HNF) liquid crystal (LC) phase is a three-dimensional (3D) helical structure composed of 2D smectic layers. Because of the complex shape of the HNF phase, it is difficult to understand the generation mechanism of HNFs in the bulk as well as in the thin-film condition. Here, we directly investigated the nucleation and growth of HNFs in nanobowls. A combination of electron microscopy and X-ray diffraction was used to reveal the transitional surface structures, in which barrel-like structures as well as short HNFs with random handedness were observed, depending on the LC film thickness. These results will be useful in achieving a better understanding of thin film structures of complex chiral structures in soft matter.