In after effects it would be as easy as using any sort of stroke or write-on effect with the Roughen Edges effect applied and then you could use that layer to matte your logo. (You could either apply the Set Matte effect to the logo or you could use the paint/marker as a Track Matte for your logo layer.)
- The Great Szalam
(The 'Great' stands for 'Not So Great, in fact, Extremely Humble')
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