Here's a crazy bit of perl

perl -lane '
    BEGIN {
        @criteria = (
            sub {shift() < -0.5},
            sub {shift() > 1},
            sub {shift() > 2},
        )
    }
    @filtered = ();
    for $i (0..$#F) {
        push @filtered, join ";", grep {$criteria[$i]->($_)} split /;/, $F[$i];
    }
    print join " ", @filtered;
' file | column -t

-0.6;-0.56  10.4;5.1  3;4
-0.9        2.4       10

Here's a crazy bit of perl

perl -lane '
    BEGIN {
        @criteria = (
            sub {shift() < -0.5},
            sub {shift() > 1},
            sub {shift() > 2},
        )
    }
    @filtered = ();
    for $i (0..$#F) {
        push @filtered, join ";", grep {$criteria[$i]->($_)} split /;/, $F[$i];
    }
    print join " ", @filtered;
' file | column -t

-0.6;-0.56  10.4;5.1  3;4
-0.9        2.4       10

This more accurately reflects your requirements

perl -lane '
    sub criteria {
        $_[0] < -0.5 and
        $_[1] > 1    and
        $_[2] > 2
    }

    @data = map {[split /;/]} @F;
    @filtered = map {[]} @F;

    for ($i = 0; $i < @{$data[0]}; $i++) {
        @tuple = map {$data[$_][$i]} (0..$#F);
        if (criteria(@tuple)) {
            push @{$filtered[$_]}, $tuple[$_] for (0..$#F);
        }
    }
    print join " ", map {join ";", @$_} @filtered;
' file