If I understand correctly you would like to create a matrix of zeros or ones based upon the results of your which call. If so, ifelse() will probably be a better option as ifelse(C>5,0,1) returns the exact vector you would like so all you would need to do is combine all of those vectors together. You didn't supply your list of "C" vectors, so I wrote a quick function to generate some vectors to show you how this can work:
> #function to generate a "C" vector
> makeC <- function(x){
+   set.seed(x)
+   round(runif(10,0,10))
+ }
> 
> #create a list of "C" vectors
> c.list <- lapply(1:5,makeC)
> #look at list of your vectors that you want binary indices
> c.list
[[1]]
 [1] 3 4 6 9 2 9 9 7 6 1
[[2]]
 [1] 2 7 6 2 9 9 1 8 5 5
[[3]]
 [1] 2 8 4 3 6 6 1 3 6 6
[[4]]
 [1] 6 0 3 3 8 3 7 9 9 1
[[5]]
 [1]  2  7  9  3  1  7  5  8 10  1
> #make a list of your binary indices
> c.bin.list <- lapply(c.list,function(x) ifelse(x>5,1,0))
> #lookat your list of binary indices
> c.bin.list
[[1]]
 [1] 0 0 1 1 0 1 1 1 1 0
[[2]]
 [1] 0 1 1 0 1 1 0 1 0 0
[[3]]
 [1] 0 1 0 0 1 1 0 0 1 1
[[4]]
 [1] 1 0 0 0 1 0 1 1 1 0
[[5]]
 [1] 0 1 1 0 0 1 0 1 1 0
> #combine all of your binary indice vectors into a matrix with rbind()
> c.bin <- do.call(rbind,c.bin.list)
> #look at your matrix of binary indices
> c.bin
     [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,]    0    0    1    1    0    1    1    1    1     0
[2,]    0    1    1    0    1    1    0    1    0     0
[3,]    0    1    0    0    1    1    0    0    1     1
[4,]    1    0    0    0    1    0    1    1    1     0
[5,]    0    1    1    0    0    1    0    1    1     0
> #this can also be collapsed into a one-liner
> do.call(rbind,lapply(1:5, function(x) ifelse(makeC(x)>5,1,0)))
     [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,]    0    0    1    1    0    1    1    1    1     0
[2,]    0    1    1    0    1    1    0    1    0     0
[3,]    0    1    0    0    1    1    0    0    1     1
[4,]    1    0    0    0    1    0    1    1    1     0
[5,]    0    1    1    0    0    1    0    1    1     0