We use a compact chirped-pulse amplified system to harmonically generate ultrashort pulses for aerosol fluorescence measurements. The seed laser is a compact, all-normal dispersion, mode-locked Yb-doped fiber laser with a 1050 nm center wavelength operating at 41 MHz. Average powers of more than 1.2 W at 525 nm and 350 mW at 262 nm are generated with <500 fs pulse durations. The pulses are time-stretched with high-dispersion fiber, amplified by a high-power, large-mode-area fiber amplifier, and recompressed using a chirped volume holographic Bragg grating. The resulting high-peak-power pulses allow for highly efficient harmonic generation. We also demonstrate for the first time to our knowledge, the use of a mode-locked ultraviolet source to excite individual biological particles and other calibration particles in an inlet air flow as they pass through an optical chamber. The repetition rate is ideal for biofluorescence measurements as it allows faster sampling rates as well as the higher peak powers as compared to previously demonstrated Q-switched systems while maintaining a pulse period that is longer than the typical fluorescence lifetimes. Thus, the fluorescence excitation can be considered to be quasicontinuous and requires no external synchronization and triggering.