Fangraphs assigns a FV (future value) to each prospect which is their projection of how good he can be based on tool and perfomance. It is on the 20-80 scale. 50 being major league regular/average, but if you notice in the rankings this is not their ceiling, it is the mid-line projection.
Then each FV is assigned a dollar figure in terms of the value of a X FV prospect.
If you click on the "Craig Edwards values" link you get an explanation of how they turn rankings into dollar values. Vlad Jr. is number 1 at $112 million. The system had Sixto valued at $53 million, Medina at $40 million, and Bohm at $25 million (note they just had Bohm ranked after Medina before the season. It is possible they have changed that).
Then they show the value of draft slots that theoretically will be added to the system. The number one pick has an average value of $45 million. Our number one is valued at $19 million. This is based on the expected WAR for each draft slot and the value of WAR. Plus some complicated math.
Obviously it is a numeric-heavy system crafted on top of subjective player rankings (i.e. the FV designations). But at least they are transparent about how they do it.