The dual-line and depressed-cladding waveguides are fabricated by femtosecond laser (fs-laser) in Er3+, MgO co-doped nearly stoichiometric LiNbO3 (Er3+:MgO:NSLN) crystals. Single-mode propagation at 1064 nm can be supported inside both two waveguides, in which the 980 nm excited green up-conversion emission can be enhanced. The confocal micro-photoluminescence (µ-PL) spectroscopy has been performed to investigate the changes of Er3+ fluorescence properties in fs-laser modified regions. Under 980 nm excitation, the fluorescence intensity of green up-conversion and near-infrared (NIR) emission is reduced by ~5% in modified areas. However, there is an increase for intensity of 532 nm excited Er3+ emission line (at ~1550 nm). Our work paves a way for fabricating novel waveguide amplifiers as well as lasers, and studying physical mechanism on fs-laser-processing of Er3+:MgO:NSLN crystals.