Per the original screenplay, Bruce is using a combination of an x-ray scanner and a supercomputer to map the pieces together, remove the deformation (caused by the impact) which then reveals any fingerprints on the bullet itself.
The 'experiment' simply seems to be him working out the best settings to use for the scanner by seeing how far the bullet fragments are likely to have spread inside the bricks (e.g. so he doesn't end up trying to do a jigsaw with pieces from several different puzzles).
As the wall samples still smoke, Wayne steps up, carrying the
sample from the crime scene. Comparing its spread to the new
samples, he selects two and carries them to an X-RAY SCANNER.
The machine gives the samples a 3-axis scan- HI-RES 3-D
IMAGES of the bullet fragment arrays come up on the screen...
The official novelisation basically repeats what's in the script. I've added it for completeness.
He held the slug up to each of the newly made holes in the walls, then selected two of the bricks and took them to an x-ray scanner. He toggled a switch and high-resolution, three-dimensional images of the bullet fragments lit up the screen.
An hour later, Bruce was standing next to Lucius Fox at the Applied Sciences Division of Wayne Enterprises. They were standing in front of another screen, and Fox was saying, “Here’s your original scan and”—he pushed a button and a second image appeared on the screen—“here it is reverse-engineered.”
Fox pushed another button, and the images began moving, seeming to assemble themselves into whole bullets. Finally, the movement stopped; one of the images bore an array of swirling lines.
“And here,” Bruce said, “is a thumb print.”