Main among them are whether to seek the death penalty for the attacks, which killed three people; whether 19-year-old Tsarnaev's case would be moved outside Boston in order to assure a fair trial, the potential consequence of authorities' decision not to read Dzhokhar Tsarnaev his 'Miranda rights'.
The Miranda rights is a warning given by police in the US to criminal suspects in their custody before they are interrogated to preserve the admissibility of their statements against them in criminal proceedings.
Several lawyers said the trial of Timothy McVeigh, the bomber of the Oklahoma City federal building, was moved to Colorado.
"It's six degrees of separation, like the Oklahoma bombing," said Max D Stern, a Boston defence attorney.
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"Everybody knows somebody who knows somebody that was injured or was there or was terrorised by what happened. Or everyone has been there, to the spot in the Marathon where it happened," Stern was quoted as saying by the 'Boston Globe'.
Carmen Ortiz, the US attorney in Massachusetts, declined to say when charges would be brought, or which crimes would be included, but said her office was "formulating the charges".
Massachusetts does not permit the death penalty for defendants charged in state courts, but federal prosecutors can seek capital punishment for crimes that include the deadly use of weapons of mass destruction.
Defendants in potential death penalty cases receive two appointed lawyers, one of whom must have experience in defending capital cases.
Dzhokhar and his brother Tamerlan Tsarnaev, 26, are accused of planting two bombs near the marathon finish line on last Monday, leaving three people dead and injuring over 180. Tamerlan was killed in a gun battle with police.