There is no reason to use a temporary file. Just assign the results of the `naviseccli ...` into an array and loop through that array. Just replace the

my $navicmd = `naviseccli -address $spa -user $nviusr -password $nvipw
+d -scope global clone -listclone -Name "$name" -cloneid $copies{$clTy
+p} -Clonestate -PercentSynced`;
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by

my @navicmd = `naviseccli -address $spa -user $nviusr -password $nvipw
+d -scope global clone -listclone -Name "$name" -cloneid $copies{$clTy
+p} -Clonestate -PercentSynced`;
[download]

remove all the file fiddling and replace

while (<FILE>) {
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by

foreach (@navicmd) {
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You might also want to rename that variable, because it doesn't contain any command, but rather the output or results of some command.