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.