The EDQM has recently published a document entitled "Guidance for electronic submissions for Certificates of Suitability (CEP) applications" (PA/PH/CEP (09) 108, 3R) in which the authority describes the requirements to be considered for the submission of an application for a CEP. Let us give you the most important message straight away: the EDQM now only accepts CEP applications in the electronic format since June 1st 2016.
Only the following formats are authorised within an application procedure: PDF, NeeS (non-eCTD electronic submission), VNeeS (the respective application format for veterinary purposes) and eCTD. A change of format during an ongoing application procedure is allowed whereas coming back to the original format isn't. Basically, the EDQM recommends the use of the eCTD with an exception though: CEP applications for the TSE risk of an API have to be submitted in the PDF format.
The guideline extensively describes how a CEP application should look like with regard to its content and structure. This is illustrated by 5 annexes which present the structure and level of granularity (degree of division in subchapters) of the different formats. The sixth annex ("Main issues which may lead to blocking a submission for its format and causing delays") lists the problems which may lead to delays in the application procedure with the respective reasons and solutions presented in a table. For example, typical errors in the electronic submission are on the one hand those which complicate the navigation through the application (inappropriate level of granularity, annexes not incorporated in the CTD structure, incorrect designation of PDF bookmarks, etc.) and on the other hand those which disrupt the lifecycle of the application in the eCTD format (wrong sequence of the chapters, incorrect attributes, e.g. "New" instead of "Replace" when replacing a leaf).
Generally, the standards applicable for the electronic submission of an application for a marketing authorisation of medicinal products must also be fulfilled in a CEP application. The "Electronic Standards for the Transfer of Regulatory Information" (ESTRI) have been elaborated by ICH's M2 Expert Working Group and are available on a separate website: the ESTRI webpage.
Now, the electronic submission of a CEP application can be done via the "Common European Submission Platform" (CESP) of the EDQM. First, a registration on the "Common European Submission Portal" is necessary. If it's not possible, there are other alternatives: secured drop-box (the EDQM provides the access data on request), CD-ROM, DVD and USB stick. Password protection or encodings must be removed first.