Is there a template to follow for what clauses to be audited internally? We have recently transitioned to Rev D, and I would like to understand better what specific clauses need to be audited annually, between each surveillance audit.
Actually, AS9100 Rev D does not use the word annual when talking about auditing. The requirements of the standard are that you conduct audits at planned intervals to determine if the QMS meets the requirements of the organization and the international standard and assess the performance indicators to judge if the QMS is effectively implemented and maintained. The standard then proceeds to talk about having an audit program based on the importance of the processes, changes affecting the organization and the results of previous audits.
So, if you are performing process audits there is nothing stating that these audits need to happen annually, and it is up to you to determine what needs to be audited during a given audit year. It could even be argued that a company could skip an extremely stable p rocess and not audit it during a year if they chose, although it is very common for every process to be audited yearly.
For more about auditing in AS9100 Rev D see these articles: https://advisera.com/9100academy/knowledgebase/6-main-steps-in-the-internal-audit-according-to-as9100-rev-d/ and https://advisera.com/9100academy/knowledgebase/developing-an-internal-audit-checklist-for-as9100-rev-d/