We introduce a versatile, robust, and integrated technique to selectively fill fluid into a desired pattern of air holes in a photonic crystal fiber (PCF). Focused ion beam (FIB) is used to efficiently mill a microchannel on the end facet of a PCF before it is spliced to a single-mode fiber (SMF). Selected air holes are therefore exposed to the atmosphere through the microchannel for fluid filling. A low-loss in-line tunable optical hybrid fiber device is demonstrated by using such a technique.