You can specify an exclude field:
Excludes: A list of class names that should be excluded from execution analysis. The list entries are separated by a colon (:) and may use wildcard characters (* and ?). (Default: empty)
However, it might be easier to use their options for classpath matching:
Only path entries matching: Comma separated list of strings that must match with the class path entry. A class path entry matches the filter, if it contains one of the given strings. (e.g. "src/main/java", Default: no filter)
See eclemma - how to ignore source about how to ignore src folders.
Also please note their caution,
Warning: If your settings do not match any of the class path entries in your project(s), every new launch in coverage mode will have an empty analysis scope.