Nickel (Kobo's operating system), by default, does not allow the user to export their annotations. However, the feature can be enabled by adding some code. Similar to enabling full screen mode, to remove both header and footer, the user needs to add the following code to the bottom of Kobo eReader.conf using a text editor (the file is located in .kobo\Kobo):
With the feature activated, a new option appears to export all annotations to a text file. After exporting the annotations, it is then possible to access the text file in the Kobo drive. For further options, please visit this MobileRead thread.