The 80-hour standoff started early Wednesday. On Friday, security forces launched 'Operation Maximus' to storm the hideout.
Security forces have found the bodies of two men and a woman inside the duplex house at the Barahaat neighbourhood, counter-terrorism unit chief Monirul Islam told reporters on Saturday.
After the assault on the Nasirpur terror den ended on Thursday, mutilated bodies of seven persons, including children were found. Police said they blew themselves up to avoid capture.
On Friday, SWAT personnel and the counter-terrorism unit launched the assault on the duplex house in the town, half a kilometre away from the Sylhet-Moulvibazar Highway.
Intermittent blasts and intense gunfire continued throughout the day. The assault was postponed in the evening due to bad weather.
Their identity was yet to be confirmed, but Islam claimed that one of them were 'directly involved' in the March 25 blasts on the street outside a terror den in Sylhet, where the army commandos were conducting an assault.
The twin blasts left seven persons dead, including the RAB Intelligence chief and two police inspectors.
The militants were asked to turn themselves in. "We wanted to capture them alive, they were asked to surrender. But they did not respond," DIG Islam said hinting that they were suicide blasts.
Heavy gunfire could be heard soon after 'Operation Maximus' was launched on Friday morning. Smoke could be seen coming out of the two-story building. At least three blasts were heard later in the day.
Islam said that they took extra precautions keeping in mind the experience in Sylhet.
He said that the assault was conducted keeping in mind the matter of civilian security.