You can exclude files and/or packages from Flex PMD by creating your own rule set, use the "exclude-pattern" tag to exclude files.
XML:
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<ruleset name="myruleset"
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xmlns=...>
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<description>My ruleset</description>
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<exclude-pattern>.*/some/package/.*</exclude-pattern>
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<exclude-pattern>.*/some/other/package/FunkyClassNamePrefix.*</exclude-pattern>
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<include-pattern>.*/some/package/ButNotThisClass.*</include-pattern>
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<rule>...
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</ruleset>
Link: http://pmd.sourceforge.net/howtomakearuleset.html
