A robust method to selectively attach specific fluorophores onto the individual cores of a multicore fiber is reported in this Letter. The method is based on the use of ultrafast laser pulses to nanostructure the facet of the fiber core, followed by amine functionalization and sensor conjugation. This surface-machining protocol not only enables precise spatial selectivity, but it also facilitates high deposition densities of the sensor moieties. As a proof of concept, the successful deposition of three different fluorophores onto selected cores of a multicore fiber is demonstrated. The protocol was developed to include attachment of a fluorescence-based pH sensor using the ratiometric carboxynapthofluorescein.