How can fill the data in region of interest matrix from original matrix data for taking average of two different time of satellite data??

I have crop the region of interest from the satellite data and also attached the two figures of different time but problem is that these latitude and longitude shows different scan number and pixel number in each orbit(day), I want to calculate mean of these data, For this i want to fill these data in new matrix (like example attached matrix), so both matrix will be in same latitude, longitude and size, so that i can easily calculate mean of these data but I am unable to this. simply I want to convert Structured Grid into Rectilinear Grid. Thank you in advance. first to figure for 11 and 16 july and last one figure is region of interest, I want to fill data in this. I am also attaching figures data (variable--latitude(row shows scan and column shows pixel), longitude(row shows scan and column shows pixel) , data(sp))) and region of interest data.