Not sure I see the problem. You apparently have cross sections in say x and y, presumably, at various values for z. That means you know the boundary of that cross sectional shape in the form of a piecewise linear polygonal shape. So use a tool like polyarea, to compute the area of each cross section in the (x,y) plane. Now, apply rectangle rule, or better yet, perhaps trapx, to integrate in the z dimension.
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