A spanwise heterogeneity of roughness is known to lead to the formation of large-scale secondary motions. In the present work the secondary motions are investigated based on the data sets extracted from direct numerical simulations (DNS) of fully developed turbulent open channel flow where spanwise-alternating streamwise stripes of rough and smooth surfaces with variation of the smooth surface elevation are introduced. In order to study the character of the secondary flow structures, the resultant flow fields are further analysed by means of instantaneous flow topology and by decomposition of the bulk mean velocity into its contribution parts. It is found that the wall-normal position of the smooth stripes significantly alters the secondary motion topology and strength of the motions. This alteration is also reflected in the fact that different volume flow rates are realized for different elevation heights of the smooth surface although the effective friction Reynolds numbers is kept constant.