but later on if I want to clear all of them how should I go about it?

The simplest way is to scope them such that they get reinitialised by re-entering the scope each time you want to re-use them:

for( some loop condition or contruct ) {
    my( %hash1, %hash2, %hash3 );
    ## do stuff with them ...
}
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Each time that loop iterates, the hashes will be reinitialised for you.

But, it you really need to do it manually, you could use:

undef %$_ for \(%h1,%h2,%h3);
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