an array of array would be by far the easiest solution with regards to actually retrieving data, however, the fact that the coordinates are fractional makes this rather complicated. if the fractions remain limited to 1 or 2 digits it'd still be workable to use ie an array whose values are then divided by 100.
the other approach would be to simply run through the file, one line at a time, and to split() the line into $x, $y and $beans, after which you simply add it to a 1-dimensional hash using ie $beancounter{$x}{$y} = $beans;
hope that helps a bit