Hi,
I am not sure I understand what you mean as a 3D field. Cloud fraction is available and can be output on pressure levels.
CLD FRAC ON P SFCS in the wrf_cntrl.parm
For example, here is example UPP output using ncl_filedump (requires NCL to dump the file this way) of TCDC on isobaric levels TCDC(press,lat,lon).
float TCDC_P0_L100_GGA0 ( lv_ISBL7, lat_0, lon_0 )
center : US National Weather Service - NCEP (WMC)
production_status : Operational products
long_name : Total cloud cover
units : %
_FillValue : 1e+20
grid_type : Gaussian latitude/longitude
parameter_discipline_and_category : Meteorological products, Cloud
parameter_template_discipline_category_number : ( 0, 0, 6, 1 )
level_type : Isobaric surface (Pa)
forecast_time : 0
forecast_time_units : hours
initial_time : 10/03/2016 (00:00)