How can I remove 0 (no data) from the matrix of an ncfile imported in matlab outside the boundary of India?

Matlab is reading the data in my ncfile for India as a matrix of 61*61, the rows and columns without data are filled with zeroes which I want to exclude from statistical analysis. How do I remove the zero or use that data for Indian region only? Replacing with NaN is an option but I think some of the values inside the Indian boundary which are zero may also get replaced? what do I do?