If the entire column is empty, try this: read the entire array once (saves file operations), and go over the array with a for loop, depending on the number of columns you want. For each column, use a case structure with a shift register to determine if the column is empty and if it is, don't insert it into the new array. If you want to build the array column by column from the file, do the same thing when reading the file. Here's an example.
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