There are two stages, the initial alignment, and then keeping alignment during soldering.
Machines are necessary for volume runs, but for prototypes a microscope will suffice for initial alignment. You need to have the board marked with alignment marks. This should be in copper, not legend, so there is no build up of tolerance between different layers.
Solder paste on the pads will be sticky enough to retain most ICs in sufficient alignment in the short trip between the microscope and the oven. As the solder melts, the strong surface tension forces will improve the alignment, pulling the IC terminals into the centres of the copper pads.
An alternative to relying on the stickiness of solder paste is to glue the IC in position. This obviously needs to be done more accurately, as the solder process will not improve the alignment.