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We propose a novel system for low-cost multi-color Fused Filament Fabrication (FFF) 3D printing, allowing for the creation of customizable colored filament using a pre-processing approach. We developed an open-source device to automatically ink filament using permanent markers. Our device can be built using 3D printed parts and off-the-shelf electronics. An accompanying web-based interface allows users to view GCODE toolpaths for a multi-color print and quickly generate filament color profiles. Taking a pre-processing approach makes this system compatible with the majority of desktop 3D printers on the market, as the processed filament behaves no differently from conventional filaments. Furthermore, inked filaments can be produced economically, reducing the need for excessive purchasing of material to expand color options. We demonstrate the efficacy of our system by fabricating monochromatic objects, objects with gradient colors, objects with bi-directional properties, as well as multi-color objects with up to four colors in a single print.