In 2009, I went to tax consultant and he has filled my 2009 taxes under resident.. but I was in F1 student visa status for entire year 2009. After going to through IRS website I came to know that he should have filled me has a non-resident. .

This time for 2010 I am planning to fill taxes has Non-resident. So do you think change of status from Resident in 2009 to Non-resident in 2010 will create any problems like IRS rejecting my 2010 filling or withholding my returns for 2010. Or should I fill 2010 tax under resident status ?

In 2010 till September I was in F1 visa status from October my status got changed to H1B.

In short : From 2008 to September 2010 - F1 student visa in US
From October 2010 to present - H1B working visa in US

In 2008 taxes filled under Non-resident (under F1 student visa status)
In 2009 taxes filled under resident (under F1 student visa status)
In 2010 taxes filled under Non-resident (under F1 student visa status & H1b working visa)


Any suggestions or comments will be highly appreciated.

Thanks
Fido

you are still a non-resident alien for 2010.
You should amend your return for 2009 to a non-resident return.
Fill out a complete 1040NR or 1040NR-EZ and form 8843 and a form 1040X.