I don't see an scenario where you might want to group an indeterminate number of rows in your dataset as features of a given class. They are either independently associated with a class or they are all features and therefore an unique row. Something like:
Instead of
xcor ycord depth
45 10 10
5 20 87
10 51 44
Would be something like:
xcor1 ycord1 depth1 xcor2 ycord2 depth2 xcor3 ycord3 depth3
45 10 10 5 20 87 10 51 44
This is pretty much the same approach that is used to model time series