The Spain international was ruled out of this summer's World Cup after suffering medial ligament damage during a Bundesliga clash with Hoffenheim in March.
Sammer insisted that Thiago's rehabilitation is going as planned but refused to confirm if the midfielder will be fit for the start of the new season.
"The operation went well," the former Germany sweeper told reporters on Wednesday.
"It will still take him a while to return, but we're giving him all the time in the world."
Thiago joined Bayern on a four-year contract from Barcelona last summer for a reported fee of €25 million (£19.8m).