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Madjid,
Consider using TOUGH2's MESHMAKER (see Appendix F of the manual) to generate a rectangular XYZ mesh as a starting point. Then use program AddBound or DeleteElements to cut out your trapecoid model domain (use option "polygonial prism" to defined an essentially arbitrary domain). Both programs can be downloaded for free at http://esd.lbl.gov/research/projects/tough/licensing/free.html.
You may also consider other pre-processing software; see http://esd.lbl.gov/research/projects/tough/software/processors.html.
Stefan