If you set c=1, lengths and time have the same unit. In HEP the most convenient one is 1 \; \mathrm{fm}=10^{-15} \mathrm{m} (femtometer, usually also called Fermi). Also obviously mass, energy, and momentum have the same unit. For this one uses \mathrm{MeV} or \mathrm{GeV}. Of course, c=1 is the "natural setting" for all relativistic physics, be it in the classical or the quantum description.
In quantum physics one more fundamental constant enters the game, Planck's "quantum of action", h. Since it turned out that it is much more convenient not to use frequency but angular velocity, nowadays we only use \hbar. The natural choice in quantum physics is then of course \hbar=1. An action has the dimension of \mathrm{length} \times \mathrm{momentum} or \mathrm{time} \times \mathrm{energy}. Now, if \hbar=1 these products are dimensionless, and thus, we need only one unit for energies, momenta, and masses. Times and distances are then measured in inverse energy units, or you argue the other way around and use a length and distance unit and measure energies, masses, and momenta in inverse length units. It depends on the context what's more convenient. Often one uses a mixed system, using fm for lengths and times and GeV for energy, momenta, and masses.
To convert from these natural units to good old standard units, you only need the "conversion factor", \hbar c \approx 197 \; \mathrm{MeV} \, \mathrm{fm}=0.197 \; \mathrm{GeV} \, \mathrm{fm}.