The following are observations from personal experience. The mechanics of barefoot running differ considerably from running with shoes - any shoes. The adaptation is "natural" insofar as instruction as to the mechanics of running is not required - the adaptations are inherent in us, mediated to a great extent through plantar tactile feedback. The bare foot of the barefoot runner is not thick with callous and inflexible as many has speculated. This is because abrading of the plantar surface is low when barefoot. Sensory thresholds direct you to minimize abrasion, but accomplishing this requires muscle adaptations and learning (coordination), both of which take time. The transition period requires a minimum of weeks even if barefoot locomotion is attempted daily. Once adapted, safe barefoot locomotion can be sustained with a few sessions per week. Obviously, more is better. Barefoot weight bearing is useful when not running, as well.
Walk before you run. Most of the muscular adaptations required for barefoot running can be acquired more safely through barefoot walking. Consider gradually increasing the duration of barefoot walking to greater than an hour, with a least three sessions per week. As comfort during barefoot walking increases, and there is no decline in comfort when bare foot walking is performed on consecutive days, it is time to increase the speed of walking. Unshod individuals transition to running from walking at a lower speed than those wearing shoes because without shoes, the extended stride causes contact with the porterior calcaneus, which is painful when barefoot. After one or two sessions at a speed just shy of feeling the desire to commence slow running, it is time to run barefoot.
In my case, I would remove my shoes for the last ten minutes of a normal run to run barefoot. Initially there is a tendency to abrade the plantar surface, hence a day or two off from running barefoot may be required initially. Otherwise, relatively brief daily runs seem adequate. Concrete and asphalt initially are easier than natural surfaces at first, because intrinsic foot muscle adaptations are required to spare the tender metatarsal-phalangeal joints through intense plantar flexion of the digits and development of these muscle take many weeks even if stimulated daily.
I have become concerned about the meager amount of weight-bearing time spent by humans particularly in industrially developed countries. There is evidence that humans evolved upright for a great part of their wakeful hours. "Anti-gravity muscles" (which includes what is commonly called "core muscles" and others used in maintaining stable equilibrium) are intensely stimulated when standing, and even more so when walking and running. These muscles are essential to safe and efficient locomotion. The sedentariness of modern human existance may be the largest hazard to safe locomotion. We all have to spend far more time upright to sustain a healthy and functional body through proper development of anti-gravity muscles. This can not be replaced with the occasional "core muscle" exercise session. This will be the subject of future site entries.