$re = '/(^[^;]+)(.*)(?:;)(.*$)?/m';
$str = 'C05-98-2;2;visakoivu, Betula pendula var. carelica;1100;1350;Hartola;1200;sv2_fi
C05-98-3;3;visakoivu, Betula pendula var. carelica;1100;1350;Savonlinna;1242;sv3_fi
C05-98-4;4;visakoivu, Betula pendula var. carelica;1100;1350;Pälkäne;1233;sv4_fi
C05-98-5;5;visakoivu, Betula pendula var. carelica;1100;1350;Savonlinna;1242;sv5_fi
C05-98-6;6;visakoivu, Betula pendula var. carelica;1100;1350;Savonlinna;1242;sv6_fi';
$subst = "[/jokupolku/$3.pdf|$1]$2";
$result = preg_replace($re, $subst, $str);
echo "The result of the substitution is ".$result;
Please keep in mind that these code samples are automatically generated and are not guaranteed to work. If you find any syntax errors, feel free to submit a bug report. For a full regex reference for PHP, please visit: http://php.net/manual/en/ref.pcre.php