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I am using NCEP/NCAR reanalysis data for mesoscale modeling at a resolution of 5 Km.

I have calculated the surface roughness for the model and using this surface roughness, I will calculate the potential zones for wind farms.

Now, I wish to use these results in microscale model which requires to downscale the data.

What methodology should I adopt?

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I don't think that rescaling of surface roughness is a very good idea. In its most basic form, roughness is variance and thus represents a statistical moment of the local scale. This is not something that would scale correctly when resampling raster resolution. The more prudent approach would be to use a DEM directly to recalculate roughness. There are many sources for global elevation data at various resolutions (30, 90, 500, 1000) so, data is readily available at a suitable resolution. The Geomorphometry & Gradient Metrics ArcGIS toolbox has a few different versions of roughness available.

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