['1', '2', '4', 'c']

Fails for condition

x[0] != "1"

as well as

x[1] != "2"

Instead of using or, I believe the more natural and readable way is:

lambda x: (x[0], x[1], x[2]) != ('1','2','3')

Out of curiosity, I compared three methods of, er... comparing, and the results were as expected: slicing lists was the slowest, using tuples was faster, and using boolean operators was the fastest. More precisely, the three approaches compared were

list_slice_compare = lambda x: x[:3] != [1,2,3]

tuple_compare = lambda x: (x[0],x[1],x[2]) != (1,2,3)

bool_op_compare = lambda x: x[0]!= 1 or x[1] != 2 or x[2]!= 3

And the results, respectively:

In [30]: timeit.Timer(setup="import timeit,random; rand_list = [random.randint(1,9) for _ in range(4)]; list_slice_compare = lambda x: x[:3] != [1,2,3]", stmt="list_slice_compare(rand_list)").repeat()
Out[30]: [0.3207617177499742, 0.3230015148823213, 0.31987868894918847]

In [31]: timeit.Timer(setup="import timeit,random; rand_list = [random.randint(1,9) for _ in range(4)]; tuple_compare = lambda x: (x[0],x[1],x[2]) != (1,2,3)", stmt="tuple_compare(rand_list)").repeat()
Out[31]: [0.2399928924012329, 0.23692036176475995, 0.2369164465619633]

In [32]: timeit.Timer(setup="import timeit,random; rand_list = [random.randint(1,9) for _ in range(4)]; bool_op_compare = lambda x: x[0]!= 1 or x[1] != 2 or x[2]!= 3", stmt="bool_op_compare(rand_list)").repeat()
Out[32]: [0.144389363900018, 0.1452672728203197, 0.1431527621755322]

Define a function to filter values:

target_list = ["FOLD/AAA.RST.TXT"]

def keep(path):
    template = get_template(path)
    return template in target_list

def get_template(path):
    front, numbers, ext = path.rsplit('.', 2)
    template = '.'.join([front, ext])
    return template

This uses str.rsplit which searches the string in reverse and splits it on the given character, . in this case. The parameter 2 means it only performs at most two splits. This gives us three parts, the front, the numbers, and the extension:

>>> 'FOLD/AAA.RST.12345.TXT'.rsplit('.', 2)
['FOLD/AAA.RST', '12345', 'TXT']

We assign these to front, numbers and ext.

We then build a string again using str.join

>>> '.'.join(['FOLD/AAA.RST', 'TXT']
'FOLD/AAA.RST.TXT'

So this is what get_template returns:

>>> get_template('FOLD/AAA.RST.12345.TXT')
'FOLD/AAA.RST.TXT'

We can use it like so:

mylist = [
    "FOLD/AAA.RST.12345.TXT",
    "FOLD/BBB.RST.12345.TXT",
    "RUNS/AAA.FGT.12345.TXT",
    "FOLD/AAA.RST.87589.TXT",
    "RUNS/AAA.RST.11111.TXT"
]

from pprint import pprint

pprint(filter(keep, mylist))

Output:

['FOLD/AAA.RST.12345.TXT'
 'FOLD/AAA.RST.87589.TXT']

You was almost there, the idea is to create a list with the functions that checks the conditions you need, once you have them you can just call those functions over the list they have to check and use all function to check if all of them are evaluated to True, note the use of partial so the function in the filter call only takes the data list; check this:

from functools import partial

ex = [
    # ["ref", "type", "date"]
    [1, 'CB', '2017-12-11'],
    [2, 'CB', '2017-12-01'],
    [3, 'RET', '2017-11-08'],
    [1, 'CB', '2017-11-08'],
    [5, 'RET', '2017-10-10'],
]

conditions  = {"ref": 3}
conditions2 = {"ref": 1, "type": "CB"}

def apply(data, *args):
"""
same as map, but takes some data and a variable list of functions instead
it will make all that functions evaluate over that data
"""
  return map(lambda f: f(data), args)


def makeConditions(p, myList):
    # For each key:value in the dictionnary
    def checkvalue(index, val, lst):
      return lst[index] == val
    conds = []
    for key, value in p.items():
        if key == "ref":
            conds.append(partial(checkvalue, 0, value))
        elif key == "type":
            conds.append(partial(checkvalue, 1, value))
        elif key == "date":
            conds.append(partial(checkvalue, 2, value))
    return all(apply(myList, *conds)) # does all the value checks evaluate to true?

#use partial to bind the conditions to the makeConditions function
print(list(filter(partial(makeConditions, conditions), ex)))
#[[3, 'RET', '2017-11-08']]
print(list(filter(partial(makeConditions, conditions2), ex)))
#[[1, 'CB', '2017-12-11'], [1, 'CB', '2017-11-08']]

Here you have a live example

Do I have to execute the filter() function for each sublist or is it possible to do it for the whole global list?

Filter iterates over all the list aplying a function for each of the elements, if the function evaluates to True then the element will remind in the result, so filter works over the whole global list