Australia completed a 5-0 clean sweep on Sunday, routing the hapless tourists for 166 off just 31.4 overs to carry off a 281-run victory in three days in the Sydney Test.
Such was the magnitude of the series defeat that major ramifications are expected for English cricket, just months after they beat Australia 3-0 in England.
Flower said he would not identify individual players facing the chop, with reports that high-profile batsman Kevin Pietersen, one of the big English failures in the series, was under pressure.
Flower, who has said he will not be standing down as team coach, said he was prepared to make tough decisions, while admitting the nightmare series was the end of an era.
Asked directly whether Pietersen would be part of England's future, Flower told reporters: "This will be a new start, and so it should be.
"It does feel like the end of some type of era. We might have to take a little more pain before we have sustained success again.
As well as speculation over the future of Pietersen, 31-year-old wicketkeeper Matt Prior, who was dropped for the last two Tests, could also face the axe.
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