Fortunately, you do not have to make all the declarations. You can use anonymous arrays (and hashes):

my %main_file = (
    USER => [ [], [], [] ],
    TEST => [ [], [], [] ],
    TRIM => [ [], [], [] ],
);
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If all the arrays are empty at the beginning, you do not have to declare anything - everything will be autovivified when dereferenced. So, in short:

my %main_file;
push @{ $main_file{USER}[0] }, $string;
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