You can see the details about the dimensions, variable etc using 'ncdisp' command.

run the following command

fid='atmPrf_C001.2012.006.11.30.G11_2010.2640_nc'

ncdisp(fid)

 Then can read each variable in matlab. Here I is the script, to display temperature profile from your data..

alt_msl=ncread(fid,'MSL_alt');

temp=ncread(fid,'Temp');

plot(temp,alt_msl)

I hope,  this will help you.