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You may file your Maryland taxes online using bFile for sales and use taxes and employer withholding taxes.
Corporation Income Tax Return should be filed by paper or efile with third party provider - see the Instruction Booklet for Corporation Income Tax - http://forms.marylandtaxes.com/07_forms/Corporation_booklet.pdf
Some specific forms and instructions may be found here - http://business.marylandtaxes.com/taxforms/08forms.asp - please be aware that not all 2008 form ar e available at this moment.
The audit is initiated by the Comptroller of Maryland - there ts a specific procedure to follow. Please find additional information here - http://compnet.comp.state.md.us/Compliance%5FDivision/General%5FInformation/Operating%5FSections/Field%5FAudit/