Planning to marry Indonesian Muslim girl.

First, I wish you both the very best as you move toward your goal as a married couple.  I will attempt to keep my response as much as possible out of the religious arena.  Although I am very much a Christian, I have had to get involved with some Sharia Law related court proceedings here in the Philippines so I speak with limited experience. 

There should be zero problems in a civil procedure if you both stick to your guns to not include the RCC or any leaders/officials and/or documents from either faith. 

No matter what, start with your "Letter of Intent to Marry" for all your official city hall visits. This letter is used to express your intent to marry and also includes your name and your fiancee's name, your signatures, and your suggested wedding dates.  All areas/Brgys will also require a Certificate of Attendance in a pre-marriage counseling, family planning, and responsible parenthood seminar (check with your city hall). 

Note: The pre-marriage counseling  is usually conducted by a Church or the DSWD for civil marriages.  This is where you may want to select your location carefully and find a pastor from a non-denominational organization or a Judge.

Here is where I will touch on religion..sorry.  Have you both considered a civil procedure where she claims non-denominational or no religion??  I Only go down this path in view of the fact her faith teaches:

"If a Muslim woman marries a non-Muslim man, knowing the ruling thereon, then she is a zaaniyah and is subject to the hadd punishment for zina. If she was unaware of the ruling, then she is excused, but they must be separated, with no need for talaaq (divorce), because the marriage is invalid in the first place." 

If she is no longer a Muslim once you are married or she has "committed hadd or zina", why must she still marry as a Muslim woman?  Clearly, Sharia Law prohibits a Muslim woman from marrying a man who is a kitabi (among the people of the book or christians) and a Muslim man or woman may not marry a mushrik [one who associates partners with God-- (i.e., Believes in Christ as part of the trinity).

Sorry, but I learned way more on this topic than I ever wanted to or imagined…  I will stop here.  Please go here for more details if you want: https://islamqa.info/en/76052

May the Father, Son and Holy Spirit always guide you both!  Take care.