To be prepared for an audit, you will need to periodically review your quality system records (DHRs) for these areas. While you can’t be certain exactly what an auditor will ask, you can use the objectives and sample questions below to review your quality system the way an auditor will during an inspection.
Also, you need to make sure you are following the FDA Quality System Regulations as defined in 21 CFR part 820
https://www.accessdata.fda.gov/scripts/cdrh/cfdocs/cfcfr/CFRSearch.cfm?CFRPart=820
Also Mock FDA audits are important for the identification of gaps in the quality systems related to medical device manufacturing. The mock FDA auditor conducts an exit meeting with the company. During this meeting, the mock auditor provides a review of major and minor findings and suggests actions to improve the issues that he or she found.
http://www.thefdagroup.com/thefdgroup-blog/2015/04/2054/