They are not done very often but certainly possible (I tried one!), involves tracking your cycle and pinpointing natural ovulation, then having the embryo transfer 3 or 5 days later. The estrogen to build the lining comes from your follicle (like any normal month), then the progesterone to convert lining and sustain early pregnancy comes from your corpus luteum (like any normal month). That means no meds at all (!) but a whole lot of monitoring to catch natural ovulation to get the transfer timing right, hoping that you ovulate at a good time and hoping the clinic will be available at the exact hour you need the embryos put in.
The alternative common, easy, fast way to do FETs is using some meds: patient takes an estrogen to suppress ovaries and build a lining, then takes a progesterone to convert the lining and sustain early pg. But this is NOT a "natural" or "unmedicated" cycle because the ovaries are suppressed, no estrogen or progesterone coming from the patient, all hormones from the meds. It is very easy on the patient, not much monitoring, no long term meds (only takes @ 2-3 weeks from start to transfer), very easy to schedule transfer. Usually the estrogen is enough to suppress, but if not the patient has to start over and take lupron too to shut down ovaries.