Anti-resonant hollow-core fiber can be used for highly sensitive gas detection, but there is a compromise between sensitivity and response time. Microchannels can be fabricated periodically through the side of anti-resonant fiber to reduce the fiber filling time, but a difficulty arises in accessing the core without disrupting the guiding structure and incurring loss. This paper presents an image processing and cross-correlation method for determining the rotational orientation of a hollow-core anti-resonant fiber without access to the local cross-section. The alignment method is demonstrated on both coated and uncoated fibers. The method allows microchannels to be accurately inserted between the capillary gaps to minimize loss. To show the adaptability of this method, microchannels with dimensions 5 × 50 µm are fabricated on both a commercial seven capillary fiber and an in-house fabricated six capillary fiber, designed for 1550 nm and 780 nm light guidance, respectively. Coated fibers were also micro-drilled, enabling superior structural integrity. Such fiber could be used for remote sensing of gas concentration, including atmospheric mapping and combustion diagnostics. The alignment method is potentially applicable for the machining of other classes of optical fibers.