A three-dimensional printer effects color changes in an extrudate using a color-application unit applying a colorant to the interior of a filament before it is melted within an extruder. Specifically, the color-application unit may receive a filament (or portions thereof) having an exposed interior surface, where color applicators are actuated to apply one or more colors to the interior surface of the filament in order to modify the extruded color. The filament may then be coupled, collapsed, or otherwise closed about the interior surface, e.g., by a mechanical coupler, to substantially enclose the interior surface of the filament, which is then fed to the extruder for fabricating a colored object in a three-dimensional fabrication process. By enclosing the colored surface within the filament before melting for extrusion, transition effects of a color change can be mitigated and transition time for a substantially complete change in color can be significantly reduced.