Depending on the size and location, you can use high dose birth control. In many situations, this will make the cyst to be reabsorbed. However if the cyst is too large or endangering your fertility, you can have it lasered off or frozen off. This is usually a keyhole surgery and does not leave a big scar.
There are several variations of the laser surgery depending on the type of cyst and how many.
Usually BC pills work really well.