Tahnks to all who replied. I used the chdir and system command to do what I wanted. Here is the script I am now succesfuly running:
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print ("\nEnter the target view ");
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chomp($target = <STDIN>);
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system("cleartool startview $target");
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print ("\nEnter the source view\n");
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chomp($source = <STDIN>);
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system("cleartool startview $source");
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print ("\nEnter VOB\n");
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chomp($vob = <STDIN>);
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system("cleartool mount \\$vob");
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$cwd = ("v:\\$target\\$vob");
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chdir ($cwd);
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system("cleartool findmerge . -ftag $source -print >> c:\\versions.txt");
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<more script> .....
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