You can apply in two ways:
After graduating high school - In this case, you may experience problems with validation of secondary education. For students outside the European Union is often necessary to recognize their secondary education at Czech secondary school designated by regional authority. For these students, it is probably easier to apply through the Johannes Kepler University in Linz.
After the successful completion of at least one semester at another university - This case is simpler because the recognition of secondary education are made by the Dean of the Faculty, ie there is no need to do a validation test in high school designated by the regional office.
The procedure for applications foreign students here.