Satellite observations of boundary layer clouds  often reveal large correlated structures (hundreds of kilometers)  which indicate the presence of strong mesoscale fluctuations.  Aircraft observations conducted in cloud topped boundary layers  reveal the same kind of phenomenon:  the existence of correlations over a much larger  distance than expected on the basis boundary layer  turbulence theory, according to which fluctuations on horizontal  scales larger than the depth of the boundary layer (typically 1km)  are supposed to vanish. 
We will show that the tendency to develop mesoscale fluctuations  also occurs in Large Eddy Simulations of (cloud topped)  atmospheric boundary layers when large domains are simulated  (several tenths of kilometers). We consider a few different  cloud topped (buoyancy driven) boundary layers (Cu and Sc).  By conducting a spectral analysis we can quantitatively  express the (sometimes dominating) presence of mesoscale  fluctuations in the various turbulence quantities.  We will discuss the differences between Cu and Sc  and will expand on the mechanism which is to be held  responsible for the generation of mesoscale fluctuations.