We have chemically modified cellulose nanofibrils (CNF) with furan and maleimide groups, and selectively labeled the modified CNF with fluorescent probes; 7-mercapto-4-methylcoumarin and fluorescein diacetate 5-maleimide, through two specific click chemistry reactions: Diels-Alder cycloaddition and the thiol-Michael reaction. Characterization by solid-state C-13 NMR and infrared spectroscopy was used to follow the surface modification and estimate the substitution degrees. We demonstrate that the two luminescent dyes could be selectively labeled onto CNF, yielding a multicolor CNF that was characterized by UV/visible and fluorescence spectroscopies. It was demonstrated that the multicolor CNF could be imaged using a confocal laser scanning microscope.