Dr. Isaacs was apparently trying to domesticate or cure the zombies using her blood, this was an early goal of umbrella after the outbreak. The purpose of the simulations they had the clones in was to test them to see how much of the Original Alice's abilities (and thereby bonding of the virus) they had, and recreate her immunity.
She then goes after Isaacs, but he manages to escape, however, not before being bitten by an advanced version of a zombie which he had tried to domesticate using blood samples from Alice's clones (which Isaacs, as seen at the beginning of the film, had been testing for any similarities to the authentic Alice's physical and mental capabilities). Those left head to the Umbrella base and the now-infected Carlos briefly kisses Alice before driving an oil truck loaded with dynamite into a horde of zombies to clear the way. The convoy leaves on helicopter while Alice stays behind. She meets with the White Queen who informs her that the cure to the infection would lie in Alice's blood.
From another wiki:
As she had not succumbed to the T-virus and transformed into a Zombie, the acquisition of Alice became a major goal to the company as a means of surviving the pandemic. Alice
After the worldwide pandemic turned most of the population into Undead, Dr. Isaacs continued Program Alice via cloning, trying to perfect a way to neutralize the Undead. Eventually, his research hit a wall, and it became necessary to find the original Alice.Project Alice
The Alice clones are perfect clones of the original Alice. They were created for several purposes, with some being test subjects for Umbrella Prime and others retaining all of the original's physical and psionic abilities. These clones were specifically created to derive a strain of the t-Virus to reverse the ravenous effects of the original virus in the undead population by increasing their intelligence.Clones
And finally, from the script:
COMMANDER OKAMOTO: And what of domestication? What news of Project Alice?
DOCTOR ISAACS: Our goals remain unchanged. The original Project Alice was unique. She bonded with the T-virus on a cellular level ... somehow managed to overcome it. Using antibodies from her blood, we could develop a serum that could not just combat the effects of the T-virus, but potentially reverse it.
DOCTOR ISAACS: Without the original Project Alice, progress has been
difficult. We have been forced to try and replicate her using cloned
genetic models ... giveng them selective memories, and actual physical
stimuli on the training floor. Trying to shortcut all the experience that led her to the point of immunity. It's laborious and the results unpredictable.
Since they didn't have the original Alice, they were not only trying to recreate her as a clone, they were trying to recreate her experiences (hence the simulation of the hive) in order to get the immunity result they wanted.