Since the Standards and Certification final rule does not include any transport standards and no EHR has been tested or certified to comply with any particular transport capability, it was unclear how the CCDs/CCRs produced by certified EHRs should be exchanged as required to attest for meaningful use.
The CMS FAQ suggests that the exchange must be accomplished over an electronic network and not using fixed media:
"No, the use of physical media such as a CD-ROM, a USB or hard drive, or other formats to exchange key clinical information would not utilize the certification capability of certified EHR technology to electronically transmit the information, and therefore would not meet the measure of this objective"
Here's my advice - do an exchange of a single CCD/CCR via a secure website, secure FTP or secure email and you'll be fine.
Although 1) certification focused on content and vocabulary standards, not transport standards and 2) certified EHRs will not be able to tell the difference between a CCD/CCR received via a network or exchanged on media, CMS has given us guidance. Also, it's a best practice to avoid the use of media for protected health information, because having clinical data on mobile media is a security risk as noted by the OIG report.