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Filtering data in multidimensional arrays

I have a 3 dimensional array, of size (20,40,13). This represents
(Flight Number, Point Number, Data Type). The flights range from 3-19.
Each flight has between 10 and 40 points. They all have the same number
of data types. Using the replicate command, I have filled the empty
array locations with -1111.

Now, I want to plot this data, with all the negative values in the first
two dimensions ('Bad Data') removed entirely. I have fooled around a bit
with WHERE, but I can only understand it when it's applied to one
dimensional arrays.

How can I use it in my particular case? Is there another solution?