The stations in the city's Wan Chai, Admiralty and Causeway Bay areas were forced to shut down on Sunday afternoon after an illegal but peaceful protest turned into a night of violence, reports the South China Morning Post.
Services were up and running again for the Monday morning commute, but several stations bore scars from Sunday's chaos.
Burn marks were seen on the ground at two entrances of Wan Chai station, where protesters had set fires and hurled petrol bombs.
Shards of broken glass at the station were also covered by white canvas, while some surveillance cameras were wrapped in black plastic.
At the Admiralty station, which also suffered heavy damage, one exit was surrounded by iron and plastic barriers, replacing the glass railings smashed by radical protesters. A surveillance camera was destroyed at another exit.
Sunday was Hong Kong's 15th straight weekend of social unrest, since the government's push for an extradition bill in June triggered a massive backlash.
The city's leader Carrie Lam has since pledged to withdraw the legislation.
Referring to incidents at the MTR stations and elsewhere, police in a statement on Monday condemned "violent acts which disregarded law and order" carried out by protesters.
At least eight people were injured, three seriously, during clashes across the city on Sunday.
( With inputs from IANS )