You need to make a new surface dataset for your case where urban is set to zero. The utility to create surface datasets has the ability to do this. Look at the CLM User's Guide about creating surface datasets. We also have a potential vegetation surface dataset that you could use, but it has other changes as well. It's here under inputdata...
$DIN_LOC_ROOT/lnd/clm2/surfdata_map/surfdata_0.9x1.25_hist_16pfts_nourb_CMIP6_simyrPtVg_c181114.nc
I'd compare it the surface dataset you used and make sure the changes are reasonable for what you want to do. Since, removing urban isn't the only thing that was done, it might not be suitable for your purposes.