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For example, I have many 3x3 arrays that I would like to store together in a single array. is this possible? if so, how would I got about doing it?

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    Yes, it's another dimension in the array. Multiple instances of a n-dimensional array stored together are a n+1-dimensional array. Commented May 4, 2016 at 18:40

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Simply:

int size = // ...
int[][][] array3d = new int[size][][];

// let's now store the arrays:
arrays3d[0] = some2darray;
// ...
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