Once you receive the Certificate of Eligibility, you need to go to the nearest Japanese Embassy or Consulate to apply for a "Student" visa.  Before going to process your application, please refer to the website of the Japanese Embassy or Consulate for more details regarding the visa application procedure.

Required documents： Passport, Photograph, Certificate of Eligibility, etc.

【Reference】
・Ministry of Foreign Affairs of Japan, Embassies & Consulates
・Ministry of Foreign Affairs of Japan, Visa

As you need to show your Certificate of Eligibility to the immigration officer at your port of entry, be sure to bring it with you.
 
(1) When entering Japan, please bring your passport, visa and Certificate of Eligibility.
(2) Show the Certificate of Eligibility to the immigration officer.
(3) After receiving an entry permit, "Permission of Landing" stamp will be affixed in your passport.  This stamp includes information regarding your "Status of Residence", "Period of Stay" and "Expiration Date of Residence Permission".