In the past Lync used txt files Company_Phone_Number_Normalization_Rules.txt to manage normalisation rules, with SFBit is now powershell Get-CsAddressBookNormalizationRule, etc.
By default it contains already some rules, but if you need to modify you can.
Here is a test tool that will show existing rules and will allow to test with a specific test number:
One thing remains unclear - the tool and all articles that I could find says that SFB will automatically strip spaces and other symboles like dashes from the phones number. However, I have an example where it does not work - when number is typed in contact lookup in SFB client the string must match exactly the string in AD phone field, otherwise the contact is not proposed. For the moment I do not know why. In another installation it work ok. It looks like something related to either client version or method (web search only) or client or GPO policy - had no time to analyse further.