two swaths matrices of latitude and longitude, How to extract the overlap parts?

Hi,

I have a problem, I have two swaths (one is a matrix of 3000 by 200 another one 9000 by 40). If I map both of them in the coast.m according to their latitudes and longitudes, the second one in like a inner band (area of the first one). I want to extract the overlapping parts (the parts of the larger band which has overlap with the smaller band within it). But this is not simple as the latitude of longitude is changing from one array to another and also the two matrices have not the same resolution (meaning the 9000 by 40 matrix in the iiner band of 3000 by 200 matrix also it has more arrays.) attached is the picture of one of the two matrices registered in the map. Would you please help me to extract the part of the bigger band which has overlap with smaller one?

Thanks in advance

Farz