How to use two dimensional arrays in legacy code?

I have a C function with a structure, inside the struct is a two dimensional array

typedef struct {
double my_array[3][3];
} my_struct;

The legacy code tool complains that it cannot accept the array with two dimensions, so I had to put the struct like

typedef struct {
double my_array[9];
} my_struct;

I was wondering if there is a way to use two dimensional arrays.