coordinates1[i][0]= Double.parseDouble(text2.substring(30,38));//X
			coordinates1[i][1]= Double.parseDouble(text2.substring(38,46));//Y
			coordinates1[i][2]= Double.parseDouble(text2.substring(46,56));//Z

How do I combine the above 3 into 1 2D array?

You already have one 2D array: coordinates1.

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