<p>My MakerBot printer supports only two filaments at the same time.</p>

<p>What are techniques to print objects with more than two colors for one object?</p>

The most obvious solution is to pause the print and swap filament for another color.
Another option is to
splice pieces of filament
together, though this does not allow very precise control of when the switch happens. There is also a device that can automatically slice filament this way.
Finally, another option that uses very little external equipment is to
use (permanent) markers to colorize light-colored filament
.
Other options include upgrading to a printer with more hotends, or installing a hotend with multiple filament inputs and one outputs, but these options would involve significantly changing your printer setup.