In the following two molecules the dissimilarity score I get between them, using the screenmd CF -M Tanimoto command, is 0.00
How it is possible since one of them has an extra carbon?
The reason why the similarity is 1.0 between the two molecules above is that in the CF fingerprint setting the size of the C chain "feature" is smaller than the length of the side chain in your example. This means that all C chains that are longer than this pre-set feature size will be identified as equal. For example if this value is 4, all C chains that are longer than 4 will be identified as equal.
I hope this helps.
Thank you very much for your answer.
One more comment: you can set this feature length in the corresponding XML config file, that is in the CFP configuration XML.