You can't shrink an array, you need to create a new one with the new size. You could do something like:
public double[] getShinkedArray(final double[] my_input_array, final int... positions) {
double[] outputArray = new double[my_input_array.length - positions.length];
for (int i = 0, j = 0; i < my_input_array.length; i++) {
if (Arrays.binarySearch(positions, i) < 0) {
outputArray[j++] = my_input_array[i];
}
}
return outputArray;
}