The suspects were arrested during Rangers raid at Nine Zero.
The FB Area and Gulgerb Town police produced the suspects at the court in a security cover provided by Rangers.
The suspects included Shakeel aka Banarasi, Muhammad Javed and Muhammad. They were accused of target killing and different crimes in the city.
After hearing arguments from counsels on both the sides, the judge remanded the suspects into police custody.
The raid on MQM headquarters, known as “Nine-Zero”, on March 11 sparked an angry response from the party, with workers shutting down large parts of Pakistan’s commercial hub.
At least one supporter of the MQM, the fourth-largest party in the national parliament, died as the paramilitary Rangers opened fire on protesting party members.