An optical chromatography system employs fluid filled hollow core fibers, such as photonic crystal fibers (PCFs), which confine an incident optical beam from a laser, for example, in the core and cause separation of particles in the fluid along the length of the PCF. The incident optical beam is confined in the fluid filled core of the PCF by a periodic lattice of air capillaries surrounding the core. The lattice either creates a lower refractive index in the cladding than in the fluid filled core or creates a 1D photonic bandgap structure where the guiding is accomplished by surrounding the fluid filled core with a periodically changing array of dielectric constant which prohibits radial dilution of the optical energy over a range of wavelengths through photonic bandgap effects.