FVCOM supports exporting to a subdomain within the main model domain. This overrides the default which is for output at all nodes and elements within the domain.

In the model namelist, add a new directive in the &NML_NETCDF section:

NC_SUBDOMAIN_FILES = 'casename_subgrd.dat'

The casename_subgrd.dat subdomain file should be formatted:

SUBDOMAIN MODE=box
UNITS=meters
TOP BOTTOM=5601046.0 5571454.0
LEFT RIGHT=406451.0 423799.0

for rectangular output; other options are available if you dig in the code. Units are the same as in the casename_grd.dat file.