Don´t know if you already read this one or if it´s what you are looking for, but there it is:
http://www.mangago.zone/read-manga/mairunovich/
http://www.mangago.zone/read-manga/ageha_100/
http://www.mangago.zone/read-manga/haru_x_kiyo/ (seen as a monster, but if you 'see' you'll see she be pretty)
http://www.mangago.zone/read-manga/gakuen_ouji/
http://www.mangago.zone/read-manga/black_rose_alice/ (nerd like teacher)
http://www.mangago.zone/read-manga/sekainohate_de_aimashou/ (unpopular guy turns into a super popular girl!)
http://www.mangago.zone/read-manga/my_boyfriend_is_a_vampire/ (guy turns girl when turns 2 a vampire)
http://www.mangago.zone/read-manga/tsuki_to_himawari/ (oneshot)
http://www.mangago.zone/read-manga/my_lovable_fatty/ (she be fat and ugly and suffer dearly 4 it, but soon she be a swan)
http://www.mangago.zone/read-manga/emma_to_hakushaku/ (ugly fat in the past, but grew pretty)
http://www.mangago.zone/read-manga/ouke_no_monshou/ (not complete, but long so find a good place 2 stop)
http://www.mangago.zone/read-manga/naisho_no_jikan/
http://www.mangago.zone/read-manga/cubism_love/ (human turned...box...er.. brain... ^^)
http://www.mangago.zone/read-manga/warau_kanoko_sama/ (she has her moments)
http://www.mangago.zone/read-manga/papillon/
http://www.mangago.zone/read-manga/black_coffee_nakano_emiko/
http://www.mangago.zone/read-manga/kujaku_no_kyoushitsu/
http://www.mangago.zone/read-manga/nil_no_koi_mahoujin/
http://www.mangago.zone/read-manga/shishi_to_cinderella
http://www.mangago.zone/read-manga/1_2_love
http://www.mangago.zone/read-manga/sylph_anthology_literature_boys/bt/11e0e8843bdc5ba5/Vol1_Ch5/pg-18/ (from this point)
http://www.mangago.zone/read-manga/hot_blooded_woman
http://www.mangago.zone/read-manga/gold_fujita_kazuko
Can someone reccomend manga where a girl is a otaku or nerd and is really ugly but then turn pretty for a reason?