Multiple steps in scaffold dissection and the construction of Scaffold trees and networks require the testing for equivalence of molecular structures. These include the enumerative generation of all possible parent scaffolds to avoid duplicates and the identification of equivalent scaffolds when merging trees or networks. In Scaffold Generator, this is done using CDK unique SMILES codes. To allow the user the definition of structural features taken into account at these steps, e.g. stereochemistry, isotopes, or aromaticity, the CDK SmilesGenerator instance employed can be set externally. By default, stereochemistry and atomic masses are not encoded but aromaticity is. The set SmilesGenerator instance is also used to create SMILES codes for origin molecules of a respective scaffold stored on nodes of scaffold trees and networks. It is important to note here that molecular characteristics of the input molecules and resulting (parent) scaffolds, like protonation states or tautomeric forms, are taken by Scaffold Generator "as is", or rather as they are represented in the chosen SMILES encoding. The only exemption is the detection of aromatic systems which is done on input structures by default. Therefore, users have to take care of preprocessing their input data sets according to their specific needs, e.g. standardising tautomeric forms and protonation states in all input molecules, before using Scaffold Generator.