You can use ncread to access your data within the netcdf file. ( From MATLAB documentation )
ncdisp('example.nc','peaks');
peaksData = ncread('example.nc','peaks');
peaksDesc = ncreadatt('example.nc','peaks','description');
surf(double(peaksData));
title(peaksDesc);
Not knowing how your data is structured within the netcdf renders a better answer impossible.