While the filament is clear, you introduce color at the beginning with the light source. It’s possible to use a number of different methods:
Colored Light Source
The fiber optic filament will transmit the color (wavelength) of the light source.
Colored LED’s are becoming a very popular fiber optic light source.
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Color Wheel or Color Filter
Adding a color filter or color wheel between the light source and the ‘starting end’ of the fiber optic filament is another popular method of introducing color
While not as popular, painting one or both ends of the fiber optic filament will also add color. Be sure to use plastic friendly paints.