Some languages have push and pop methods for dealing with arrays, but you'll have to switch to using an ArrayList if you want to do this in Processing (see the link to the Java reference description for details of available methods).  Depending on whether you want to carry out the same operations on the second level array you could probably leave that as a standard array...

For the record, in Java, a 2D array is actually an array of rows, each row being an array of values.
Their size is fixed. So to alter them, you might do the Processing way, created a new array on each transformation, and copying the relevant data there.
Java collections, as hinted above, might be more efficient.