Musharraf is stepping down to restore Pakistan to civilian rule, as demanded by his political rivals and Western allies, before parliamentary elections on January 8.
All main political parties have signed up to the elections.
However, Benazir Bhutto, the former prime ministers now in Pakistan after years in exile, said she might boycott the vote which is being orgnaised under emergency rule.
Sharif's appeal
On Tuesday Nawaz Sharif, another former prime minister returned from exile, called on Bhutto to boycott the elections.
Sharif said: "I shall try to convince Benazir Bhutto to boycott the polls."
He said he had already asked her to take a "firm stance" against the vote.
General Ashfaq Kayani, a former intelligence chief, will replace Musharraf as army commander.
Kayani holds a positive reputation with Western leaders and has worked with Bhutto in the late 1980s.
On Thursday, Musharraf will be sworn in as civilian president, his spokesman said.
He gained a second five year term after pro-Musharraf judges validated his October 6 election victory.
Swat valley deaths
The developments formed a backdrop to claims by the Pakistani army that it has killed 45 fighters loyal to Maulana Fazlullah, a pro-Taliban religious leader, in the Swat valley in the North West Frontier Province.
Troops secured a key strategic mountain overlooking opposition strongholds, officials said on Tuesday.
"We have secured Najia hilltop and Gunj, Usmani-Sar and Segram hills from the militants," Major Amjad Iqbal, a military spokesman, said.
Four soldiers were also killed in the fighting.
The army also said that they had shut down a pirate radio station used by Fazlullah.
The movement of fighters supporting Fazlullah into the Swat valley has increased concern of unrest spreading to previously calm regions.