Senior UCI and World Anti-Doping Agency officials will meet in Russia next week to discuss potential appointments to a three-member expert panel, McQuaid told The Associated Press.
Long-standing claims about the UCI and Armstrong's relationship "absolutely will be addressed" by the commission, he said.
They include allegations of collusion over suspicious test results at the 1999 Tour de France and 2001 Tour of Switzerland, plus cash donations to UCI totalling $125,000 from the now disgraced rider.
"I would be very sure that the audit will show that there's nothing untoward ever been done with Armstrong," McQuaid said in an interview on the day the UCI published a report it commissioned to consult cycling stakeholders and fans after the Armstrong affair.
Armstrong declined comment Thursday to the AP.
Among six "critically important" points in the report by consultants Deloitte, the UCI was told to work more closely with WADA and the U.S. Anti-Doping Agency. The U.S. body had testy relations with the UCI during the investigation which detailed systematic doping by Armstrong and his teams.
The UCI should act quickly and clearly in deciding how to probe "historic doping cases," which could involve offering amnesties to riders and officials, Deloitte said after processing 6,369 survey responses and conducting a series of working groups.
"Any ultimate decision should be made only after consultation with WADA and USADA," Deloitte said in a report summary published by the UCI. The 12-page document did not mention Armstrong's name.
The UCI appears to be rebuilding relations with USADA by meeting a request to provide laboratory results of urine and blood samples given by Armstrong during his career.
McQuaid, who met USADA chief executive Travis Tygart last week in Brussels, said the UCI and WADA-accredited labs were searching their archives for information.
"From what I am told, in the coming weeks it should come to USADA in batches," he said.
The independent panel should take shape next week in St. Petersburg, on the sidelines of an Olympic gathering attended by UCI director general Christophe Hubschmid and WADA counterpart David Howman.
McQuaid said the two organizations, which have sparred in public, have met regularly since committing in January to an independent audit of the UCI's anti-doping program and decision-making during the period of Armstrong's career.
"The UCI and WADA are talking about names of who might do that (work)," said McQuaid, who in January closed down a previously appointed commission which was investigating if cycling leaders protected the American rider from scrutiny during his 1999-2005 run of Tour de France wins.
The latest panel will is likely to include two officials experienced in anti-doping science and sports law.
"Experts in this field who therefore know what they are looking for, and what they are looking at and understand all the files they will be reading," McQuaid said. "The UCI will maintain that any decisions we took at the time were taken within the rules at the time, with all the knowledge we had at the time.
"I think it's important that an audit can show that."
McQuaid plans to announce the panel members after a scheduled June 12-13 meeting of the UCI's management board in Bergen, Norway. Their audit report is expected within several months.
"After that, we will discuss what further measures we need to take in relation to looking at the past and dealing with the past," he said.
McQuaid declined to set deadlines, but agreed the UCI hopes to close the Armstrong affair this year.
"Of course we would," he said, pointing to the consultants' findings. "This report talks about a bright future for cycling and that is what I want to concentrate on."
The UCI board could act soon on some of Deloitte's 11 highest-priority suggestions, by hiring a newly-retired professional racer as Rider Relationship Manager and doing more to develop women's cycling.
In Norway, the UCI could explore creating an independent tribunal to hear doping cases after research revealed little support for national federations continuing to prosecute and impose lenient sanctions on riders who are often national heroes.
McQuaid said a working group would be needed to suggest funding and operating a tribunal.
At the UCI congress in Italy in September, McQuaid aims to create a commission overseeing all women's cycling. Currently, women's races are managed alongside the men's in disciplines such as road, track and cyclocross.
In Italy, McQuaid will seek a third four-year term and is currently the only candidate despite widespread criticism.
Deloitte's top priority for the UCI is restoring credibility, including "public perception" of its anti-doping efforts and "current UCI leadership."
"I have no problem if a rival comes forward and no problem with a good, healthy debate on the future of the sport, and no problem defending my work over the past eight years" McQuaid said. "It's not the leadership of the UCI that has damaged the sport, it's other individuals."
Among more than 5,600 cycling fans and 731 "cycling family" members, including 133 professional riders, responding to Deloitte, 72 per cent acknowledged that measures to combat doping have improved since 2008.
Still, "72 per cent of respondents rated the UCI's performance in fighting against doping as either 'poor' or 'very poor,'" the report said.
AP Sports Writer Jim Vertuno in Austin, Texas, contributed to this report