The clue book in the Library gives you a set of course headings and distances to a series of locations, which turn out to be holes in the ground.
Once you can work out how to measure distance using the numbered flags around the cage at the link in point, following the directions, if done carefully, will lead you to the holes. But this is very difficult to do, especially on the later holes, which have many changes of direction. Small errors build up, and you can end up quite a long way off.
Best bet, seems to be to draw out the courses and plot a direct line from the cage to each hole, and try to go straight there in one move.
Hole 1 is the easiest in Minkata and most people can almost fall into by accident, even if they haven't figured out the clue book yet, because it is so close to the link in point. To borrow a golfing term, this hole is "Stroke Index 5".
In fact, if know what you're looking for, you can see it from the top of the cage:
Notice that the hole appears white on top, rather than the dark surface that the other "craters" or "stumps" have.