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Usually foundy specifies the vth depending on w and L of devices you are going to use.
If you go through the BSIM3v3 manual, you would find that the threshold voltage is a function of loads of other parameters.
And the value you would observe in the model file is for hand calculations when you do design.
A question what percentage variation did you observe.
Holberg in his book has mentioned on how one should characterise a mos device, kindly go through that, it would be great help to you.
Hope it helps.