I want to know if it is allowed to underline with pen translations / explanations or tafseer of Holy Quran?
Of course it's permissible, they're just like any other book!
In many verses of Quran, such as the following ones, Allah has told us to think deeply about what it states.
أَفَلَا يَتَدَبَّرُونَ الْقُرْآنَ أَمْ عَلَىٰ قُلُوبٍ أَقْفَالُهَا
Then do they not reflect upon the Qur'an, or are there locks upon [their] hearts?
أَفَلَا يَتَدَبَّرُونَ الْقُرْآنَ ۚ وَلَوْ كَانَ مِنْ عِندِ غَيْرِ اللَّـهِ لَوَجَدُوا فِيهِ اخْتِلَافًا كَثِيرًا
Then do they not reflect upon the Qur'an? If it had been from [any] other than Allah , they would have found within it much contradiction.
إِنَّا جَعَلْنَاهُ قُرْآنًا عَرَبِيًّا لَّعَلَّكُمْ تَعْقِلُونَ
Indeed, We have made it an Arabic Qur'an that you might understand.
So do you think if underlining helps your understanding of Quran, God will punish you for that?
I don't think so :)