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[thredds] using the netcdf subsetting service

I've got the Thredds Data Server installed and I'm trying to use it to subset a 3D grid (depth, latitude, longitude) large netcdf file. The netcdf file was generated by a third parties software, and is probably not compliant with anything. As subset of its schema is shown below.
If I rename some coordinate variables, I should be able to make it compliant with some convention. My question is how do I most efficiently extract a 3D subset? I want to extract a subset of depth as well as a subset of longitude and latitude. 

Any ideas would be most appreciated.
Thank you.
Eric.

netcdf d7110.subvol {
dimensions:
        TIMESTEP = 1 ;
        LONGITUDE_T = 481 ;
        LATITUDE_T = 241 ;
        LONGITUDE_U = 481 ;
        LATITUDE_U = 241 ;
        DEPTH = 66 ;
        DEPTH_EDGES = 67 ;
variables:
        int TIMESTEP(TIMESTEP) ;
                TIMESTEP:long_name = "Timestep" ;
        float LONGITUDE_T(LONGITUDE_T) ;
                LONGITUDE_T:long_name = "Longitude" ;
                LONGITUDE_T:units = "degrees" ;
                LONGITUDE_T:Format = "F10.4" ;
        float LATITUDE_T(LATITUDE_T) ;
                LATITUDE_T:long_name = "Latitude" ;
                LATITUDE_T:units = "degrees" ;
                LATITUDE_T:Format = "F10.4" ;
        float DEPTH(DEPTH) ;
                DEPTH:long_name = "Depth" ;
                DEPTH:units = "cm" ;
                DEPTH:Format = "F5.2" ;
                DEPTH:positive = "down" ;
                DEPTH:edges = "DEPTH_EDGES" ;
        float POTENTIAL_TEMPERATURE__MEAN_(DEPTH, LATITUDE_T, LONGITUDE_T) ;
POTENTIAL_TEMPERATURE__MEAN_:long_name = "potential temperature 
(mean)" ;
                POTENTIAL_TEMPERATURE__MEAN_:units = "C" ;
                POTENTIAL_TEMPERATURE__MEAN_:_FillValue = 0.f ;
                POTENTIAL_TEMPERATURE__MEAN_:LEVEL = 0 ;
                POTENTIAL_TEMPERATURE__MEAN_:T_GRID = -1 ;
 ....
}


**********************************************
Eric Davies, M.Sc.
Barrodale Computing Services Ltd.
Tel: (250) 472-4372 Fax: (250) 472-4373
Web: http://www.barrodale.com
Email: eric@xxxxxxxxxxxxx
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Mailing Address:
P.O. Box 3075 STN CSC
Victoria BC Canada V8W 3W2

Shipping Address:
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University of Victoria
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