Medical implants are prone to colonization by bacterial biofilms, which are highly resistant to antibiotics. Normally, surgery is required to replace the infected implant. One promising non-invasive treatment option is to destroy the biofilm with high-intensity focused ultrasound (HIFU) exposure. In our study, Pseudomonas aeruginosa bacterial biofilms were grown on graphite disks in a flow chamber for three days prior to exposing them to ultrasound pulses of varying duration or burst period. The pulses were 20 cycles in duration at a frequency of 1.1 MHz from a spherically focused transducer (f/1, 63 mm focal length), creating peak compressional and rarefactional pressures at the disk surface of 30 and 13 MPa, respectively. P. aeruginosa were tagged with GFP and cells killed by HIFU were visualized using propidium iodide, which permeates membranes of dead cells, to aid determining the extent of biofilm destruction and whether cells are alive or dead. Our results indicate that a 30-s exposure and 6-ms pulse period or those combinations with the same number of pulses, were sufficient to destroy the biofilm and to kill the remaining cells. Reducing the number of pulses decreased biofilm destruction, leaving more dead and live bacteria on the surface.